title: Nociceptor, juvenile RAMA responder 7

status: Public on Jul 21 2020

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina BaseCaller: Sequence images to BCL files
Illumina bcl2fastq v2.17.1.14: Demultiplexing to fastq files
FastQC v0.11.5: Quality checks
STAR aligner v2.5.2a: alignment to reference genome Mus musculus mm10 version 96, allowing for 2 mismatches within 50 bases
R v3.6.1, edgeR v3.22.5: read count analysis and TPM calculation
Genome_build: mm10 version 96
Supplementary_files_format_and_content: Text files containing tab-delimited matrices of raw read counts or Transcripts Per Million (TPM)

growth_protocol: DRG were isolated from male C57BL/6J mice at the indicated ages. In brief, DRG neurons were promptly isolated and digested with collagenase (Life Technologies) and papain (Worthington). Neurons were plated on poly-D-lysine (1 mg/mL, Milipore) coated coverslips, which were additionally coated with laminin (20 µg/mL, Life Technologies). Growth medium (Ham’s F12/DMEM 1:1 ratio with L-glutamine; Gibco) was supplemented with 10 % horse serum (Life Technologies) and 100 ng/ml NGF, 50 ng/ml GDNF, 50 ng/ml BDNF, 50 ng/ml NT-3, and 50 ng/ml NT-4 (all growth factors procured from R&D Systems). Experiments were performed 24 h after culturing to ensure reliable adhesion to the coated surface before mechanical stimulation. See Coste et al., 2010; Narayanan et al., 2016; Narayanan et al., 2018; Michel et al. 2020.

extract_protocol:
After patch clamp recordings negative pressure was applied to the patch pipette in whole-cell-mode to aspirate cytosolic contents as suggested (Fuzik et al., 2016; Cadwell et al., 2017). The content of the patch pipette was transferred, by applying positive pressure, to a 1.5 ml centrifuge tube filled with 100 µl of cool lysis buffer containing TCEP from the NucleoSpin RNA XS kit (MACHEREY-NAGEL GmbH & Co. KG, Germany). Often, pipettes were broken inside the tube to ensure full transfer of cellular material to the buffer. After harvest samples were flash frozen in liquid nitrogen and stored at -80 °C. RNA purification was performed according to the manufacturer’s instructions of the NucleoSpin RNA XS kit (MACHEREY-NAGEL GmbH & Co. KG, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols. The workflow was performed at NGS Integrative Genomics (NIG) core (University Medical Center Göttingen, UMG). For cDNA synthesis the SMART Ultra Low Input RNA kit for Illumina Sequencing (Clontech Laboratories, Inc., USA) was used according to the supplier’s protocol. Clean-up reactions were done with AMPure XP beads (Beckman Coulter Genomics, UK). For library preparation the Nextera DNA Sample Prep kit (Illumina, Inc., USA) was used in combination with Illumina-compatible adaptors and PCR primers from Integrated DNA Technologies, Inc., USA. Libraries were assessed by a Fragment Analyzer using the Agilent High Sensitivity DNA analysis kit and Kapa Biosystems Illumina library Quantitation kit. Libraries were sequenced on the HiSeq4000 sequencing system (Illumina, single-end 50 bp fragments).

treatment_protocol: DRG neuron somata were mechanically stimulated using a blunt glass probe at -70 mV holding potential and room temperature up to 11 µm in standard NaCl-based bath solution and standard KCl-based pipette solution in whole-cell voltage clamp. Action potentials were evoked using current injection in whole-cell current clamp experiments under the same conditions. Action potentials were categorized as noci or mec according to their waveform (full width at half maximum and presence of a bump in the falling phase); categories given here match the resulting RNA-profile (expression of common marker genes). Please see for details: Michel et al. 2020 “Maturational changes in mouse cutaneous touch and Piezo2-mediated mechanotransduction”.

tag: strain

tag: genotype

value: WT

tag: Sex

value: male

value: post natal day 28

value: dorsal root ganglion neuron

tag: action potential type

value: nociceptor

tag: mechanically activated rapidly adapting current amplitude (na)

tag: sequencing batch


title: D9

status: Public on Sep 30 2020

type: SRA

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

country: China

institute: Zhongshan Ophthlamic Center

library_source: transcriptomic single cell

data_processing:
16bp 10XBarcodes are encoded at the start of R1 file, while 8bp sample index sequences are incorporated as the i7 index read. R1 and R2 are standard illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10X Barcodes and 12 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.
Basecalls performed using CASAVA version 1.8
We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads  to achieve the clean data.
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter.Then the feature-barcode matrices were obtained by aligning reads to the mm10 genome using CellRanger v3.0.0.
Seurat package (version: 2.3.4, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with all high variable genes and top 10 principals were used for tSNE construction. Utilizing graph-based cluster method, we acquired the unsupervised the cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. logFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: MEF reprogrammed into retinal ganglion cell-like neurons

growth_protocol: MEFs were cultured in DMEM+10% FBS, at 37℃ in incubator.

extract_protocol:
10X Genomics Chromium
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.

treatment_protocol: MEFs were infected with Ascl1/Brn3b/Isl1 overexpressing lentiviruses, doxycycline was added on day 0 to induce Ascl1/Brn3b/Isl1 expression, cells were switched to neuronal medium (DMEM/F12+GlutaMAX+N2+B27+Forskolin+FGF2) on day 2 of reprogramming; medium was half-changed every other day.

tag: cell type

value: MEF

tag: reprogramming day

value: day 9


title: sc-RNAseq_CD34+ cells - 96h_lane6_donor1

status: Public on Aug 25 2020

city: Paris

first: Andràs

last: Pàldi

state: Ile de France

address: 19 rue Chaligny

department: Centre de Recherche de Saint Antoine

country: France

institute: Ecole Pratique des Hautes Etudes

description: Single-cell RNAseq

library_source: transcriptomic

data_processing:
Demultiplex according to plate barcode in read1:  cutadapt (version 2.3) with the folowing configuration > 5' & 3' triming quality cutoff ( 30,30), maximum error rate (0), trimming (no-trim), indels (no-indels), minimum read length (30:20), paired end mode (g), pair filtering mode (any)
Demultiplex according to cell barcode in read2: cutadapt (version 2.3) with the folowing configuration > 5' & 3' triming quality cutoff ( 30,30), maximum error rate (0), trimming (no-trim), indels (no-indels), minimum read length (30:20), paired end mode (g), pair filtering mode (any), modifying read name (y)
Select reads with polyT tails in read2: cutadapt (version 2.3) with the folowing configuration > maximum error rate (0), trimming (no-trim), minimum overlap (14), indels (no-indels), paired end mode (g ^NNNNNNNNNNTTTTTT )
Select reads mapping on ERCC Spike-in genome: bowtie2 (version 2.3.5.1) with the folowing configuration > dovetailing read pairs (-- dovetail), discordant pairs (--no-discodant), individual mates (--no-mixed)
Mapping remaining reads to reference genome: STAR (version 2.7.0a) with the folowing configuration > Maximum number of output alignments for multi-mappers (1)
Genome_build: hg19
Removing chr y: R (version 3.6.3) dplyr (version 1.0.0)
Filtering cells: R (version 3.6.3) dplyr (version 1.0.0) > minimum number of read per cell (80 000), maximum % of mitochondrial reads (10), ERCC spike correlation (Pearson > 0.6)
Filtering genes: R (version 3.6.3), dplyr (version 1.0.0) > gene type (protein coding), transcript status (known), minimum number of read per gene (2), minimum number of UMI per gene (2)
Pseudotiming and clustering: Matlab (version 2018b), Calista (version 1.2.2)
Supplementary_files_format_and_content: Tab seperated raw count matrix (STAR output) (donor 1 & donor 2)
Supplementary_files_format_and_content: Tab seperated file count matrix after filtering  (donor 1 & donor 2)
Supplementary_files_format_and_content: Tab seperated and normalized count matrix for Calista top 200 gene (donor 1)
Supplementary_files_format_and_content: Tab seperated and normalized count matrix for Calista top 200 gene (donor 2)

organism: Homo sapiens

source_name: Umbilical cord blood

growth_protocol: CD34+ cells were purified from human healthy cord blood with a two-step immunomagnetic beads protocol and were then frozen in a cryopreservation medium. After thawing, CD34+ cells were cultured in a 96-well plate in a humidified 5% CO2 incubator at 37°C. Cells were grown in prestimulation medium made of X-Vivo (Lonza) supplemented with penicillin/streptomycin (respectively 100U/mL and 100µg/mL - Gibco, Thermo Scientific), 50 ng/ml h-FLT3, 25 ng/ml h-SCF, 25 ng/ml h-TPO, 10 ng/ml h-IL3 (Miltenyi) final concentration.

extract_protocol:
Single cells were marked with 7AAD to remove dead cell by FACS sorting. Cells were individually sorted into 96-well plates containing 4µL of lysis buffer (using Triton 100% as lysis reagent) Supplemented with RNase inhibitor (RNaseOUT, Thermo scientific) and specific barcoded RT primers.
Single-cell RNA sequencing was performed as described in "Jaitin et al.Science, 2014 Feb 14; 343(6172): 776–779" with minor adaptations.

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium until lysis was performed. Cells were collected and lysed from 5h up to 96h of cytokine stimulation.

tag: tissue

value: Blood

tag: disease state

value: Healthy

tag: treatment

value: Untreated


title: sc-RNAseq_CD34+ cells - 5h_lane7_donor2

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 72h_lane6_donor1

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 24h_lane7_donor2

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 48h_lane6_donor1

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 24h_lane6_donor1

description: Single-cell RNAseq


title: sc-RNAseq_CD34+ cells - 5h_lane6_donor1

description: Single-cell RNAseq


title: Nociceptor, juvenile RAMA responder 3

country: Germany

tag: age

value: post natal day 26


title: Nociceptor, juvenile RAMA responder 5

value: post natal day 27


title: sc-RNAseq_CD34+ cells - 96h_lane5_donor1

description: Single-cell RNAseq


title: Nociceptor, juvenile RAMA responder 4


title: sc-RNAseq_CD34+ cells - 24h_lane5_donor1

description: Single-cell RNAseq


title: Mechanoreceptor, adult RAMA responder 5

value: post natal day 85

value: mechanoreceptor


title: bulk-ATACseq_CD34+ cells - 48h_donor3

description: Bulk ATAC seq

library_source: genomic

data_processing:
TN5 Adapter trimming: cutadapt with the following configuration > adapter type (Non-internal 5’ adapter "AGATGTGTATAAGAGACAG;max_error_rate=0.1;min_overlap=10"), 3' end quality cutoff (20), minimum read length (18)
Sequences alignement:  Bowtie2 (version 2.3.4.2) with the following configuration > Genome index (UCSC_GRCh37_hg19), maximum fragment length for valid paired-end alignments (800)
Remove duplicate: picard MarkDuplicates (version 2.18.11) with the following configuration > remove duplicate (TRUE), validation stringency (SILENT)
Random BAM downsampling to 16M reads (without disrupting pairs of reads): samtools (version 1.9)
Peak calling on downsampled BAM: MACS2 (version 2.1.2) with the following configuration > format of input file (BAMPE), mappable genome (hs), broad peak calling (broad), p-value cutoff (0.1)
Motif analysis: HOMER (version 4.11) with the following configuration > size of the region for motif finding (size given), number of motif to find (100)
Intersection of peaks within a time point & union of peaks accross two consecutive time points: R (version 3.5.1) & GenomicRanges (version 1.34.0)
Feature count (read attribution to peaks): R (version 3.5.1) & Rsubread (version 1.32.2) with the following configuration > Paired End (TRUE), count chimeric fragmeent (FALSE), count multi-mapping reads (TRUE)
Differential analysis (number of reads in peaks as a proxy for accessibility quantification): R (version 4.0.1) & DEseq2 (version 1.28.0) with the following configuration > seqtype (paired-end), control (t), treated (t + 1)
Supplementary_files_format_and_content: Peak text files generated with downsampled BAM files
Supplementary_files_format_and_content: Tab delimited text file containing HOMER transcription factor binding motifs enrichment results for "known motifs"
Supplementary_files_format_and_content: Matrix table with read counts in the region resulting from the intersection of peaks detected in every sample for each time point
Supplementary_files_format_and_content: Matrix table with read counts in the region resulting from the union of peaks detected in every sample for two consecutive time points
Supplementary_files_format_and_content: Tab delimited text file with pValue and fold change for peaks union of every sample for two consecutive time points
Supplementary_files_format_and_content: Tab delimited text file with peak informations and genome features attribution

molecule: genomic DNA

extract_protocol:
A one-step gentle membrane permeabilization and DNA transposition was performed by adding 50µl transposition mixture (25 µL TD buffer 2X, 2,5µL of transposase TDE1 (Illumina), 0,5 µL digitonin 0,1% (Promega) and 22 µL water) to the cell pellets and by incubating at 37°C for 30 minutes under agitation.
Libraries were prepared according "Fast -ATACseq" protocol described in "Corces et al, Nat Genet. 2016 Oct; 48(10): 1193–1203".

treatment_protocol: Cells were stimulated with cytokines after thawing and were grown in the same medium until lysis was performed. Cells were collected and lysed from 0h up to 48h of cytokine stimulation.


title: Mechanoreceptor, adult RAMA responder 2

value: post natal day 115


title: Mechanoreceptor, adult RAMA responder 4


title: Mechanoreceptor, adult RAMA responder 1


title: bulk-ATACseq_CD34+ cells - 5h_donor3

description: Bulk ATAC seq


title: bulk-ATACseq_CD34+ cells - 24h_donor1

description: Bulk ATAC seq


title: Nociceptor, adult RAMA responder 4


title: Nociceptor, adult RAMA responder 3

value: post natal day 102


title: Nociceptor, adult RAMA responder 2

value: post natal day 92


title: bulk-ATACseq_CD34+ cells - 0h_donor3

description: Bulk ATAC seq


title: Nociceptor, adult RAMA responder 5

value: WT


title: Nociceptor, juvenile RAMA responder 6

value: male


title: Nociceptor, adult non-responder 3

value: post natal day 90

value: no


title: Nociceptor, adult non-responder 7

value: post natal day 101

value: dorsal root ganglion neuron

value: nociceptor


title: Brain, 5XFAD-R47H_Ab1-48-1

status: Public on May 13 2020

city: South San Francisco

first: Meer

last: Mustafa

state: CA

address: 131 Oyster Point Blvd, Ste 600

country: USA

institute: Alector

data_processing:
10X Genomics' produced libraries were sequenced on a Illumina NovaSeq flow cell…
cellranger v3.1.0 was used to align FASTQs into UMI count matrices. Default parameters for cellranger count was used and aligned to the mm10 genome builld…
To add hTREM2 expression, FASTQs were aligned to the hg38 genome…
Individual mice data was subset based on criteria mentioned in the paper to microglia cells only
For further processing, see Methods in publication.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: 5XFAD-*.tsv:  Tab-delimited gene x single-cell ID UMI count matrix for all Cd45+ cells
Microglia_*.tsv.gz:  pair of processed files are a subset of cells from each of the 11 5XFAD-*.tsv files.

molecule: polyA RNA

source_name: whole brain

extract_protocol:
The whole brains of 22 week-old (5.5 month) mice from AL002c or control IgG treated groups were dissected after transcardial perfusion with ice-cold PBS and dissociated. Immune cells were recovered following Percoll (GE) separation and subset via FACS for Cd45+ cells. More details are in the Methods.
PCR addition of Illumina adapters

tag: antibody

value: R47H (TREM2 variant)

value: whole brain

tag: cell population

value: Cd45+ cells


title: Brain, 5XFAD-R47H_Ab1-7-5


title: bulk-ATACseq_CD34+ cells - 0h_donor2

description: Bulk ATAC seq

value: Blood

value: Healthy

value: Untreated


title: Brain, 5XFAD-R47H_Ab2-10-7

value: Isotype


title: Brain, 5XFAD-CV_Ab1-5-2

value: CV (TREM2 variant)


title: bulk-ATACseq_CD34+ cells - 5h_donor2

description: Bulk ATAC seq


title: Nociceptor, juvenile RAMA responder 2

value: post natal day 28


title: Tgfbr2_M1

status: Public on May 06 2020

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

data_processing:
Grooming of de-multiplexed reads was performed with FASTQ groomer 1.04.
Mapping was done using TopHat2 0.7.
Transcript abundance estimation and differential expression significance testing were computed with Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Output file from Cuffdiff

source_name: Endothelial cells

extract_protocol:
Total RNA was obtained with Qiagen RNAeasy Plus Micro kit
The cDNA was synthesized with SMART-Seq v4 Ultra Low Input RNA Kit. Libraries were constructed with Nextera XT DNA Library Prep Kit using the cDNA as input.

tag: genotype/variation

value: lacking Tgfbr2

tag: organ

value: Brain


title: Nociceptor, juvenile RAMA responder 1

value: WT

value: male


title: Mechanoreceptor, adult RAMA responder 7

value: post natal day 85

value: mechanoreceptor


title: Mechanoreceptor, adult RAMA responder 6

value: post natal day 115

value: dorsal root ganglion neuron


title: Mechanoreceptor, adult RAMA responder 3

value: post natal day 89


title: Nociceptor, adult RAMA responder 9

value: post natal day 90

value: nociceptor


title: Nociceptor, adult RAMA responder 6


title: Nociceptor, adult RAMA responder 7


title: Nociceptor, adult RAMA responder 1


title: Nociceptor, adult non-responder 6

value: post natal day 84

value: no


title: Nociceptor, adult non-responder 5

value: post natal day 93


title: Nociceptor, adult non-responder 4


title: Nociceptor, adult non-responder 1


title: het4

data_processing:
Grooming of de-multiplexed reads was performed with FASTQ groomer 1.04.
Mapping was done using TopHat2 0.7.
Transcript abundance estimation and differential expression significance testing were computed with Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated data containing raw counts for all the gene features for each sample.

value: heterzygote


title: Nociceptor, adult RAMA responder 8


title: Brain, 5XFAD-R47H_Ab2-49-3

value: Isotype

value: R47H (TREM2 variant)

value: whole brain

value: Cd45+ cells


title: Brain, 5XFAD-R47H_Ab2-53-4


title: het2

value: Brain


title: Brain, 5XFAD-R47H_Ab1-54-2


title: het1


title: Nociceptor, adult non-responder 2

value: WT

value: male


title: Brain, 5XFAD-CV_Ab2-4-4

value: CV (TREM2 variant)


title: Brain, 5XFAD-CV_Ab2-3-3


title: Brain, 5XFAD-R47H_Ab1-8-6


title: L75P-9_d170-3

status: Public on Jan 15 2020

city: Baltimore

first: Alyssa

last: Kallman

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University, School of Medicine

description: single cell RNA

data_processing:
Fastq files were processed and filtered according to the Dropseq cookbook version 1.0.1
processed reads were aligned to GRCh38 using the STAR RNA aligner
exons were tagged using the Homo_sapiens.GRCh38.88.gtf annotations file
Genome_build: GRCh38
Supplementary_files_format_and_content: raw UMI count matrices with genes as rows and cells as columns

source_name: stem cell derived retinal organoid

growth_protocol: Embryoid bodies (EB) were lifted with either 2 mg ml-1 dispase or ReLeSR and weaned into Neural Induction Media (NIM: DMEM:F12 1:1, 1% N2 supplement, 1x MEM nonessential amino acids (MEM NEAA), 1x GlutaMAX and 2 mg ml-1 heparin (Sigma)) over the course of 4 days.  On day 6 (d6), 1.5 nM BMP4 (R&D Systems) was added to fresh NIM and on d7, EBs were plated on Matrigel at a density of 200 EBs per well of a 6-well plate.  Half the media was replaced with fresh NIM on d9, d12 and d15 to gradually dilute the BMP4 and on d16, the media was changed to Retinal Differentiation Media (RDM: DMEM:F12 3:1, 2% B27 supplement, MEM NEAA, 1X antibiotic, anti-mycotic and 1x GlutaMAX). On d25-30, optic vesicle-like structures were manually dissected and maintained as free floating organoids in poly HEMA (Sigma)-coated flasks with twice weekly feeding of 3D-RDM (RDM + 5% FBS (WiCell), 100 mM taurine (Sigma) and 1:1000 chemically defined lipid supplement) to which 1 mM all-trans retinoic acid (Sigma) was added until d100

extract_protocol:
Organoids were dissociated to single cells with papain (Worthington) to 1 mg ml-1 and 5 μL DNase (Roche) per mL, using 200 μL papain mix per organoid.  After 1-2 hours when organoids appeared fully dissociated the reaction was quenched with media containing 10% FBS (Gibco).  Single cells were resuspended in HBSS (Gibco) and 0.1 mg mL-1 BSA at 120,000 cells per mL
Illumina nextera XT multiplexed with N70X indices according to the Dropseq protocol

tag: days in culture

tag: cell line (all ipsc)

value: L75Pfs clone 9


title: WT_d170-2

description: single cell RNA

tag: genotype


title: Brain, 5XFAD-CV_Ab1-1-1


title: Tgfbr2_M3

tag: strain

value: lacking Tgfbr2


title: Tgfbr2_M4


title: Tgfbr2_M2


title: WT d103-2

description: single cell RNA


title: L75P-7_d170-2

description: single cell RNA

value: L75Pfs clone 7


title: Tgfbr2_C3

value: controls


title: WT_d101-2

description: single cell RNA


title: Tgfbr2_C2


title: L75P-9_d170-2

description: single cell RNA


title: Tgfbr2_C1


title: L75P-9_d103-1

description: single cell RNA


title: L75P-7_d170-3

description: single cell RNA


title: L75P-9_d103-2

description: single cell RNA


title: Microglia, Input3

status: Public on Jan 06 2020

data_processing:
Demultiplexed reads were pseudo-mapped to the mouse genome using Salmon 0.13.1
Transcript abundance was summarized to gene-level using Tximport 1.12
Differential expression was analyzed with DESeq2 1.24
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated files containing counts, the output from the DESeq2 analysis (including Gene symbol, Log2Fold change, p-value, and FDR-corrected p-value)

source_name: Microglia

extract_protocol:
Ribosome-bound RNA was immunoprecipitated using anti-HA antibody and Dynabeads conjugated to Protein A. Total RNA was obtained with Qiagen RNAeasy Plus Micro kit from an Input aliquot and from the entire immunoprecipitate.
The cDNA was synthesized with SMART-Seq v4 Ultra Low Input RNA Kit. Libraries were constructed with Nextera XT DNA Library Prep Kit using the cDNA as input.

value: 5 mo

value: Microglia

tag: rip antibody


title: ko4

value: knock out


title: Microglia, IP1

value: anti-HA


title: ko3


title: Microglia, Input2


title: ko1


title: Mouse APP ASO J352

status: Public on Dec 24 2019

city: Los Angeles

first: Russell

last: Littman

state: Ca

address: 610 Charles E Young Dr S

department: Integrative Biology and Physiology

institute: UCLA

description: Drop-Seq; whole cell

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.5.0c.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital gene expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Drop-seq samples were processed using Drop-seq Tools
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. Cell names contain treatment group, sample name, and cell type

source_name: Hippocampus

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing.
Mouse Hippocampus was dissected and dissociated into single-cell suspension, followed by drop-seq library preparation. Libraries were prepared following the latest drop-seq protocol..

tag: strain/backgorund

value: Antisense oligonucleotide

value: Hippocampus

value: 10 weeks


title: het3

value: heterzygote


title: WT_d170-3

description: single cell RNA


title: ko2


title: WT_d170-1

description: single cell RNA


title: L75P-11_d100-1

description: single cell RNA

value: L75Pfs clone 11


title: Mouse APP PBS J322

description: Drop-Seq; whole cell

value: Phosphate buffered saline


title: L75P-9_d170-1

description: single cell RNA


title: L75P-7_d170-1

description: single cell RNA


title: wk2413234S

status: Public on Dec 18 2019

city: Santa Cruz

first: Christopher

last: Villarreal

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

data_processing:
Data were processed with cellranger 2.0.0 and Seurat version 2 in R, aligned to hg38. The raw counts were normalized within each sample to be a fraction of the max counts within that cell, multiplied by the median number of counts per sample, and batch was regressed out at the data scaling step. This method is the method used by Peng, et al Cell 2019, and additional details can be found in the manuscript.
Genome_build: hg38
Supplementary_files_format_and_content: The matrix includes normalized, batch corrected data.

source_name: iPS-derived cerebral organoid

extract_protocol:
single-cell dissociation
Single Cell 3' v2 Library

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

tag: protocol

value: Protocol [L]

tag: Sex

value: female


title: L13234controlweek15

tag: tissue

value: male


title: WT_d101-1

description: single cell RNA

value: WT


title: WT d103-1

description: single cell RNA


title: L75P-11_d100-2

description: single cell RNA


title: Microglia, Input1

tag: age

value: Brain

tag: cell type


title: Mouse APP ASO J361

description: Drop-Seq; whole cell

tag: treatment


title: Mouse APP ASO J351

description: Drop-Seq; whole cell


title: Mouse APP PBS J323

description: Drop-Seq; whole cell


title: chimp.iPSC.alter-medium.RNA.Rep2

status: Public on Jul 12 2019

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19,calJac3, panPan2,panTro6
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.

organism: Pan troglodytes

growth_protocol: Chimpanzee iPSCs were cultured on plates pre-coated with Matrigel (BD Biosciences) in a customized mTeSR1 medium (CTFR medium)19: mTeSR1 basal medium supplemented with FGF2 (Peprotech, 20ng/ml) and IWR1(Sigma, 2.5uM). Chimpanzee iPSCs were passaged every 5-6 days with TrypLE (Life Technologies) at a split ratio of 1:10. ROCK inhibitor Y27632 (10uM) was added at least one hour prior to and 24 hours after passaging.

extract_protocol: Total RNA was extracted with Trizol according to protocol (Thermo Scientific, 15596-026). All libraries were constructed using standard illumina TruSeq LT library prep.

tag: differentiation time

value: chimp induced pluripotent stem cell


title: Mouse APP PBS J321

description: Drop-Seq; whole cell


title: Microglia, IP2

value: 5 mo


title: wk24H1S_S2


title: wk2413234P

value: Protocol [D]


title: Nociceptor, juvenile RAMA responder 8

value: post natal day 31

value: dorsal root ganglion neuron

tag: action potential type

value: nociceptor

tag: mechanically activated rapidly adapting current amplitude (na)

tag: sequencing batch


title: Microglia, IP3

value: Microglia

value: anti-HA


title: day05.Input.Batch2.Rep1

status: Public on Jul 09 2019

data_processing:
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie2 for ATAC-seq, BWA for ChIP-seq and Hi-C, rnaSTAR for RNA-seq. Contacts for Hi-C data were stored in the juicer Hi-C format (could be opened with juicebox.jar provided by Aiden lab).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for ChIP-seq and input, juicer hic format for Hi-C data and normalized read per million kilobases (RPKM) for RNA-seq.

source_name: ES derived cardiac mesoderm

extract_protocol: The ChIP-seq has been carried out as previously described (Jolma et al., 2013;  Tuupanen et al., 2012; Yan et al., 2013). Briefly, 2 million cells were crosslinked with 1%  formadehyde for 15 min at RT. The reaction was quenched by adding 125 mM of  Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM TrisHCl  pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium  deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was  sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated  with antibodies to pull down the specific DNA bound TFs or histones. After  intensive wash, DNA was purified and prepared as sequencing library using illumina  Truseq LT kit. Several samples with different indexes were pooled together for 50 or 100  cycles of single read sequencing with illumina Hiseq 2500.

value: ES derived cardiac mesoderm

tag: genotype

value: H9 MLC2v:H2B

tag: matched input

tag: chip antibody

value: none (input)


title: day05.Input.Batch2.Rep2


title: MoDC Donor 3

status: Public on Oct 18 2019

type: RNA

city: Nantes

first: Aurelie

last: Moreau

address: 30 bd Jean Monnet

institute: INSERM U1064

description:
C3_D3
gene expression analysis of T7-amplified polyA RNA

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Blood monocytes Donor 3

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: ATDCs were differentiated following a 6 day-culture of monocytes in AIMV medium supplemented with recombinant human GM-CSF at 100U/ml. MoDC were differentiated following a 6 day-culture of monocytes in IMDM medium supplemented with 10% FBS, 1000U/ml recombinant human GM-CSF and 1000U/ml recombinant human IL-4. MoMacro were obtained following a 7 day-culture of monocytes in RPMI 1640 medium supplemented with 20% FCS and 100ng/ml rhM-CSF.

extract_protocol: Total RNA was isolated using RNeasy Plus kits (Qiagen) as previously described (Riquelme, P et al. Mol Ther., 2013).

value: whole blood

value: Monocyte-derived Dendritic Cells (MoDCs)

tag: gender


title: ATDC Donor 5

description:
C1_D5
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 5

value: Autologous Tolerogenic Dendritic Cells (ATDCs)


title: MoDC Donor 6

description:
C3_D6
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 6

value: male


title: MoDC Donor 2

description:
C3_D2
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 2


title: day80.CTCF.Rep1

source_name: ES derived ventricular cardiomyocyte

value: ES derived ventricular cardiomyocyte

value: CTCF


title: MoDC Donor 5

description:
C3_D5
gene expression analysis of T7-amplified polyA RNA


title: MoDC Donor 1

description:
C3_D1
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 1


title: chimp.iPSC.alter-medium.HiC.Rep2

description:
RH497
The processed data (chimp.hic) was generated from both replicates and is linked to the rep1 sample records

extract_protocol: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.

value: chimp induced pluripotent stem cell


title: chimp.iPSC.alter-medium.RNA.Rep1


title: chimp.iPSC.alter-medium.HiC.Rep1


title: ATDC Donor 6

description:
C1_D6
gene expression analysis of T7-amplified polyA RNA


title: day80.Input.Batch2.Rep1


title: day05.CTCF.Rep2


title: MoDC Donor 4

description:
C3_D4
gene expression analysis of T7-amplified polyA RNA

source_name: Blood monocytes Donor 4


title: ATDC Donor 4

description:
C1_D4
gene expression analysis of T7-amplified polyA RNA


title: ATDC Donor 3

description:
C1_D3
gene expression analysis of T7-amplified polyA RNA


title: ATDC Donor 1

description:
C1_D1
gene expression analysis of T7-amplified polyA RNA


title: HERV2-ins-clone2.HiC.Rep2

source_name: Embryonic stem cell

value: Embryonic stem cell

value: H9 MLC2v:H2B HERV2-ins-clone2


title: day00.SMC3.ab9263.Rep1


title: day00.Input.Batch3.Rep1


title: day05.CTCF.Rep1


title: HERV2-ins-clone1.HiC.Rep1

value: H9 MLC2v:H2B HERV2-ins-clone1


title: day00.HERV1.CRISPRi.RNA.Rep1

value: H9 MLC2v:H2B HERV1-CRISPRi


title: HERV2-ins-clone2.RNA.Rep2


title: HERV2-ins-clone2.RNA.Rep1


title: day00.HERV2.CRISPRi.HiC.Rep1

value: H9 MLC2v:H2B HERV2-CRISPRi


title: HERV2-ins-clone1.RNA.Rep2


title: HERV2-ins-clone1.RNA.Rep1


title: day00.HERV1.CRISPRi.HiC.Rep1


title: HERV2-ins-clone2.HiC.Rep1


title: marmoset.iPSC.HiC.Rep2

description: Processed data file marmoset.hic is available on GSM373496

organism: Callithrix jacchus

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: HERV2-ins-clone1.HiC.Rep2


title: day00.HERV2.KO.RNA.Rep1

value: H9 MLC2v:H2B HERV2-KO


title: day00.HERV2.CRISPRi.RNA.Rep2


title: marmoset.iPSC.HiC.Rep1

description: marmoset.hic


title: day00.HERV2.CRISPRi.RNA.Rep1


title: day00.HERV2.CRISPRi.HiC.Rep2


title: marmoset.iPSC.RNA.Rep1


title: day00.ctrl.RNA.Rep1


title: day00.HERV1.CRISPRi.HiC.Rep2


title: day00.HERV1.KO.HiC.Rep2

value: H9 MLC2v:H2B HERV1-KO


title: day00.HERV2.KO.RNA.Rep2


title: day00.HERV1.CRISPRi.RNA.Rep2


title: ATDC Donor 2

description:
C1_D2
gene expression analysis of T7-amplified polyA RNA


title: day00.HERV1.KO.RNA.Rep2


title: day00.HERV1.KO.HiC.Rep1


title: marmoset.iPSC.RNA.Rep2


title: day00.ctrl.HiC.Rep1

value: H9 MLC2v:H2B


title: day00.HERV2.KO.HiC.Rep1


title: day00.HERV1.KO.RNA.Rep1


title: day07.Input.Batch2.Rep1

source_name: ES derived cardiac progenitor cells

value: ES derived cardiac progenitor cells

value: none (input)


title: day00.HERV2.KO.HiC.Rep2


title: day00.ctrl.HiC.Rep2


title: day15.Input.Batch2.Rep1

source_name: ES derived primitive cardiomyocite

value: ES derived primitive cardiomyocite


title: day00.ctrl.RNA.Rep2


title: day15.Input.Batch2.Rep2


title: day15.CTCF.Rep2


title: day02.Input.Batch2.Rep2

source_name: ES derived mesoderm

value: ES derived mesoderm


title: day00.Input.Batch2.Rep2


title: day07.Input.Batch2.Rep2


title: day15.CTCF.Rep1


title: day07.CTCF.Rep2


title: day02.CTCF.Rep2


title: day07.CTCF.Rep1


title: day00.CTCF.Rep2


title: day02.CTCF.Rep1


title: day80.Input.Batch1.Rep1

extract_protocol: ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441).   Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the  links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf, Library preparation: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf.


title: day00.CTCF.Rep1


title: day80.Input.Batch1.Rep2


title: day15.Input.Batch1.Rep2


title: day07.Input.Batch1.Rep2


title: day15.Input.Batch1.Rep1


title: day05.Input.Batch1.Rep2

value: ES derived cardiac mesoderm


title: day07.Input.Batch1.Rep1


title: day02.Input.Batch1.Rep1


title: day05.Input.Batch1.Rep1


title: day02.Input.Batch1.Rep2


title: day00.Input.Batch1.Rep1


title: day80.H3K27ac.Rep1

value: ES derived ventricular cardiomyocyte


title: day80.H3K27ac.Rep2


title: day00.Input.Batch1.Rep2


title: day07.H3K27ac.Rep2


title: day15.H3K27ac.Rep1


title: day15.H3K27ac.Rep2


title: day00.Input.Batch2.Rep1


title: day07.H3K27ac.Rep1


title: day05.H3K27ac.Rep1


title: day00.H3K27ac.Rep1


title: day05.H3K27ac.Rep2


title: day80.RNA.Rep2


title: day80.RNA.Rep1


title: day02.H3K27ac.Rep2


title: day00.H3K27ac.Rep2


title: day15.RNA.Rep1


title: day02.H3K27ac.Rep1


title: day15.RNA.Rep2


title: day05.RNA.Rep1


title: day05.RNA.Rep2


title: day02.RNA.Rep1


title: day00.RNA.Rep1


title: day80.HiC.Rep1


title: day15.HiC.Rep1


title: day07.HiC.Rep2


title: day07.HiC.Rep1


title: day05.HiC.Rep1


title: day02.HiC.Rep2


title: day02.HiC.Rep1


title: day00.HiC.Rep2


title: day07.RNA.Rep1


title: day00.HiC.Rep1


title: bonobo.iPSC.mTeSR1.RNA.Rep2

organism: Pan paniscus

growth_protocol: Chimpanzee and bonobo iPSCs were cultured on plates pre-coated with Matrigel (BD Biosciences) in commercial mTeSR1TM medium (Stemcell technology, 85850). Cells were passaged every 5-6 days with TrypLE (Life Technologies) at a split ratio of 1:10. ROCK inhibitor Y27632 (10uM) was added at least one hour prior to and 24 hours after passaging.


title: chimp.iPSC.mTeSR1.RNA.Rep2


title: chimp.iPSC.mTeSR1.HiC.Rep2

description: chimp.mt.hic on Series record


title: chimp.iPSC.mTeSR1.RNA.Rep1


title: day07.RNA.Rep2


title: chimp.iPSC.mTeSR1.HiC.Rep1

description: chimp.mt.hic on Series record


title: bonobo.iPSC.mTeSR1.RNA.Rep1


title: day80.HiC.Rep2


title: bonobo.iPSC.mTeSR1.HiC.Rep1

description: bonobo.hic on Series record


title: day00.RNA.Rep2


title: day02.RNA.Rep2


title: day15.HiC.Rep2


title: E15 progenitor in E12 brain IL10_PoolA

status: Public on Jun 28 2019

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Reads were aligned with STAR aligner
The count matrix were generated with HTSeq
cells expressing less <2000 genes or >12% of mitochondrial RNAs were excluded
Cell cycle correction with ccRemover R package
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files with cell cycle removed log2 RPM values for each cells

source_name: Neuronal progenitors

extract_protocol:
SMART-Seq v4 3’ DE Kit
Single cells were collected into tubes and the library was constructed with Nextera XT library prep kit according to manufacturers

tag: strain

tag: condition

value: Transplanted

value: E15 (in E12 environment)


title: E15 progenitor in E12 brain IL10_PoolB


title: E15 progenitor in E12 brain IL12_PoolA


title: E15 progenitor in E12 brain IL09_PoolH


title: E15 progenitor in E12 brain IL11_PoolA


title: E15 progenitor in E12 brain IL09_PoolD


title: E15 progenitor in E12 brain IL09_PoolC


title: day05.HiC.Rep2


title: bonobo.iPSC.mTeSR1.HiC.Rep2

description: bonobo.hic on Series record


title: E15 progenitor in E12 brain IL09_PoolA


title: E15 progenitor in E12 brain IL07_PoolC


title: E15 progenitor in E12 brain IL08_PoolG


title: E15 progenitor in E12 brain IL08_PoolD


title: E15 progenitor in E12 brain IL08_PoolH


title: E15 progenitor in E12 brain IL06_PoolG


title: E15 progenitor in E12 brain IL07_PoolH


title: E15 progenitor in E12 brain IL09_PoolB


title: E15 progenitor in E12 brain IL05_PoolE


title: E15 progenitor in E12 brain IL05_PoolG


title: E15 Flash Tag IL12_PoolC

value: WT


title: E15 Flash Tag IL12_PoolE


title: E15 Flash Tag IL12_PoolF


title: E15 Flash Tag IL11_PoolH


title: E15 Flash Tag IL12_PoolB


title: E15 Flash Tag IL11_PoolG


title: E15 Flash Tag IL11_PoolF


title: E15 Flash Tag IL11_PoolE


title: E15 Flash Tag IL10_PoolE


title: E15 Flash Tag IL10_PoolH


title: E15 Flash Tag IL10_PoolD


title: E15 Flash Tag IL10_PoolC


title: E15 Flash Tag IL11_PoolD


title: E15 Flash Tag IL11_PoolC


title: E15 Flash Tag IL09_PoolF


title: E15 Flash Tag IL10_PoolF


title: E15 progenitor in E12 brain IL06_PoolD


title: E15 Flash Tag IL12_PoolG


title: E15 progenitor in E12 brain IL05_PoolH


title: E15 Flash Tag IL08_PoolB


title: E15 Flash Tag IL09_PoolE


title: E15 Flash Tag IL08_PoolF


title: E15 Flash Tag IL02_PoolA


title: E15 Flash Tag IL08_PoolA


title: E15 Flash Tag IL07_PoolB


title: E15 Flash Tag IL01_PoolD


title: E15 Flash Tag IL03_PoolA


title: E12 Flash Tag IL07_PoolG


title: E12 Flash Tag IL07_PoolA


title: E15 Flash Tag IL06_PoolC


title: E12 Flash Tag IL04_PoolA


title: E12 Flash Tag IL04_PoolB


title: E12 Flash Tag IL05_PoolF


title: E12 Flash Tag IL05_PoolD


title: E12 Flash Tag IL04_PoolE


title: E12 Flash Tag IL05_PoolB


title: E12 Flash Tag IL02_PoolD


title: E12 Flash Tag IL03_PoolF


title: E12 Flash Tag IL03_PoolC


title: E12 Flash Tag IL02_PoolF


title: E12 Flash Tag IL02_PoolG


title: E12 Flash Tag IL01_PoolH


title: E12 Flash Tag IL03_PoolE


title: E12 Flash Tag IL02_PoolE


title: E12 Flash Tag IL01_PoolE


title: E12 Flash Tag IL06_PoolA


title: E12 Flash Tag IL01_PoolG


title: YH10PWeek8

status: Public on Jun 14 2019

data_processing:
Data were processed with cellranger 2.0.0 and Seurat version 2 in R, aligned to hg38.  The raw counts were normalized within each sample to be a fraction of the max counts within that cell, multiplied by the median number of counts per sample, and batch was regressed out at the data scaling step. This method is the method used by Peng, et al Cell 2019, and additional details can be found in the manuscript.
Genome_build: hg38
Supplementary_files_format_and_content: The matrix includes normalized, batch corrected data.

value: iPS-derived cerebral organoid

tag: donorid

tag: cloneid

tag: age (weeks)

value: Directed [D]

value: Male


title: YH10SWeek10

tag: tissue

tag: protocol

value: Least Direct [L]

tag: Sex


title: Week10S_1323_4

value: Female


title: H1XWeek8

source_name: hES-derived cerebral organoid

value: hES-derived cerebral organoid

value: Most Directed [M]


title: Week10P_1323_4


title: E12 Flash Tag IL05_PoolC

tag: age


title: H1XWeek10


title: H28126S2Week10


title: H1SWeek5


title: H1XWeek3


title: H28126S2Week5


title: H1SWeek8


title: H1SWeek10


title: H1SWeek3


title: H28126S2Week8


title: H28126PWeek5


title: H28126XWeek3


title: H28126XWeek5


title: H28126XWeek10


title: H28126XWeek8


title: H28126SWeek3


title: H28126SWeek8


title: H28126SWeek10


title: Week5P_1323_4


title: H28126PWeek8


title: Week8P_1323_4


title: H1XWeek5


title: Week8S_1323_4


title: Week5S_1323_4


title: YH10PWeek10


title: YH10PWeek5


title: YH10SWeek8


title: YH10SWeek5


title: P15 T2MG 1

status: Public on Jan 10 2019

data_processing:
Grooming of de-multiplexed reads was performed with FASTQ groomer 1.04.
Mapping was done using TopHat2 0.7.
Transcript abundance estimation and differential expression significance testing were computed with Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output for all the comparisons are contained in the processed data spreadsheet (.xlsx). Output consists of gene identifiers, chromosome location, mean FPKM for each condition, log2 fold change, and raw and adjusted significance levels.

source_name: Microglial cells

extract_protocol:
RNA was extracted using the RNAeasy Plus Micro kit from Qiagen, following manufacturer´s instruction.
Poli-A+ libraries were constructed with Clontech SMART-Seq ultra low input kit, following manunfacturer´s instruction.

value: C57Bl6; FVB

tag: devlopmental stage

value: Microglia

tag: genotype/variation

value: lacking TGFbeta signaling


title: P60 Control 4

value: Control


title: P60 T2MG 3


title: P60 T2MG 4


title: P15 T2MG 2


title: P60 T2MG 1


title: P15 Control 1


title: P60 Control 1


title: H28126SWeek5

source_name: iPS-derived cerebral organoid


title: P15 Control 2


title: P15 Control 3


title: P60 Control 3


title: P15 T2MG 3


title: E16 Control 3


title: E16 T2MG 3


title: E16 T2MG 1


title: E16 Control 2


title: RPE1_single_MidS_09

status: Public on Dec 13 2018

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: cell type

value: Epithelial cells immortalized with hTERT

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: MidS


title: RPE1_single_MidS_12

tag: strain


title: RPE1_single_MidS_08


title: P60 T2MG 2


title: RPE1_single_MidS_14


title: RPE1_single_MidS_13


title: RPE1_single_MidS_11


title: RPE1_single_MidS_10


title: P60 Control 2


title: RPE1_single_MidS_06


title: RPE1_single_MidS_07


title: RPE1_single_G1_03

description: control


title: RPE1_single_MidS_05


title: RPE1_single_G1_02

description: control


title: E16 T2MG 2


title: SP_23WF_B1

status: Public on Jun 29 2018

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

description:
polyA RNA
SP_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include the TPM values of RefSeq genes. The cell barcode information is available in the file "Region_Sample_Barcode_Information.xlsx".  The columns of the processed data file names are organized as follows:  X(region information)_X(22 or 23W(week) F(female) or M(male))_X(batch information)_scX where 'scX' refers to the cell number and can be associated to the barcode on the third tab of "Region_Sample_Barcode_Information.xlsx". For example, sc1 = primer1, sc2 = primer2, etc.

source_name: Human Embryonic Cortex Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pipette. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

value: brain

tag: developmental stage

value: 23 week gestation

tag: gender

value: female


title: PRECU_23WM_B1

description:
polyA RNA
PRECU_23WM_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.

value: male


title: E16 Control 1


title: ST_22WF_B1

description:
polyA RNA
ST_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.

value: 22 week gestation


title: ST_23WF_B31

description:
polyA RNA
ST_23WF_B31
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: SF_22WF_B1

description:
polyA RNA
SF_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: SM_23WF_B1

description:
polyA RNA
SM_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: ST_23WF_B61

description:
polyA RNA
ST_23WF_B61
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PRC_22WF_B1

description:
polyA RNA
PRC_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: SF_23WF_B5

description:
polyA RNA
SF_23WF_B5
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PO_23WF_B1

description:
polyA RNA
PO_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PO_23WF_B4

description:
polyA RNA
PO_23WF_B4
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PC_23WF_B4

description:
polyA RNA
PC_23WF_B4
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: SM_22WF_B1

description:
polyA RNA
SM_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PO_22WF_B1

description:
polyA RNA
PO_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PC_22WF_B1

description:
polyA RNA
PC_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: RMF_22WF_B1

description:
polyA RNA
RMF_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PC_23WF_B1

description:
polyA RNA
PC_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAT_23WF_B1

description:
polyA RNA
PAT_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAT_22WF_B1

description:
polyA RNA
PAT_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAO_23WF_B4

description:
polyA RNA
PAO_23WF_B4
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAO_23WF_B2

description:
polyA RNA
PAO_23WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: SM_23WF_B4

description:
polyA RNA
SM_23WF_B4
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: P_22WF_B1

description:
polyA RNA
P_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: MT_23WF_B2

description:
polyA RNA
MT_23WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: P_23WF_B3

description:
polyA RNA
P_23WF_B3
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: M_23WF_B3

description:
polyA RNA
M_23WF_B3
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: LO_23WF_B9

description:
polyA RNA
LO_23WF_B9
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: M_23WF_B4

description:
polyA RNA
M_23WF_B4
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PO_23WF_B3

description:
polyA RNA
PO_23WF_B3
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: MT_23WF_B7

description:
polyA RNA
MT_23WF_B7
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: MT_22WF_B1

description:
polyA RNA
MT_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: LO_23WF_B6

description:
polyA RNA
LO_23WF_B6
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: M_22WF_B1

description:
polyA RNA
M_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FFA_23WF_B1

description:
polyA RNA
FFA_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FFA_22WF_B2

description:
polyA RNA
FFA_22WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FFA_22WF_B1

description:
polyA RNA
FFA_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: LO_23WF_B1

description:
polyA RNA
LO_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: BST_22WF_B1

description:
polyA RNA
BST_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: LO_22WF_B1

description:
polyA RNA
LO_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: IT_22WF_B1

description:
polyA RNA
IT_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: IP_22WF_B1

description:
polyA RNA
IP_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FFA_23WF_B2

description:
polyA RNA
FFA_23WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAO_23WF_B1

description:
polyA RNA
PAO_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: IG_22WF_B1

description:
polyA RNA
IG_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FL_22WF_B1

description:
polyA RNA
FL_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: FL_22WF_B2

description:
polyA RNA
FL_22WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: PAO_22WF_B1

description:
polyA RNA
PAO_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: CMF_23WF_B2

description:
polyA RNA
CMF_23WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: BST_22WF_B2

description:
polyA RNA
BST_22WF_B2
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: CMF_22WF_B1

description:
polyA RNA
CMF_22WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: IG_23WF_B1

description:
polyA RNA
IG_23WF_B1
The brain region of each cell is encoded in the column header of the processed data file. Please see the file "Region_Sample_Barcode_Information.xlsx" for a key to the brain regions abbreviations.


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells [ZNF382_rep5]

status: Public on Oct 25 2016

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
ChIP-seq reads were mapped to the human genome build hg19 using Bowtie 2. The 3’ end of reads were trimmed to a final length of 50 nucleotides, mapped with the Bowtie “--very-sensitive” preset of parameters, and duplicate reads were removed using SAMtools.
MACS v1.4 was used for peak calling, using experiment-specific background models constructed by pooling multiple control datasets.
Genome_build: hg19
Supplementary_files_format_and_content: MACS v1.4 output, containing the coordinates of peaks and summits based on hg19 genome assembly, as well as associated scores.
Supplementary_files_format_and_content: combined_summits.per_protein.hg19.tar: Tar of peak summits per protein.
Supplementary_files_format_and_content: combined_summits.motif_hits.per_protein.hg19.tar: Tar of motif hit locations within peaks per protein.
Supplementary_files_format_and_content: motifs.pfm.txt: Tab-delimited text file includes motifs identified for each protein.

source_name: HEK293 cells expressing GFP-tagged protein

growth_protocol: HEK293 cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum and antibiotics. Gateway-compatible entry clones were cloned into the pDEST pcDNA5/FRT/TO-eGFP vector according to the manufacturer's instructions and co-transfected into Flp-In T-REx 293 cells together with the pOG44 Flp recombinase expression plasmid. Cells were selected for FRT site-specific recombination into the genome, following instructions by the manufacturer.

extract_protocol:
Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). GFP-tagged transcription factors were immunoprecipitated with a polyclonal anti-GFP antibody (ab290, Abcam) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the TruSeq ChIP-seq library kits (Illumina) according the manufacturer's instructions followed by PCR amplification and agarose gel size selection.

treatment_protocol: Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting. HEK293 cells were cross-linked for 10 min in 1% formaldehyde.

tag: uniprotkb id

tag: cell line


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells [ZNF382_rep3]


title: ChIP-seq of GFP-tagged ZNF436 in HEK293 cells [ZNF436_rep1]


title: ChIP-seq of GFP-tagged ZNF490 in HEK293 cells [ZNF490_rep1]


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells [ZNF382_rep2]


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells [ZNF382_rep1]


title: ChIP-seq of GFP-tagged ZNF317 in HEK293 cells [ZNF317_rep3]


title: ChIP-seq of GFP-tagged ZNF317 in HEK293 cells [ZNF317_rep2]


title: ChIP-seq of GFP-tagged ZNF384 in HEK293 cells [ZNF384_rep1]


title: ChIP-seq of GFP-tagged ZFP28 in HEK293 cells [ZFP28_rep2]


title: genomic DNA from OPSCC sample, MPC_T15

status: Public on May 10 2018

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: SAMPLE 10

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities in supplementary file

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: tissue

value: oropharyngeal cancer

tag: disease state

value: cancer


title: genomic DNA from OPSCC sample, MPC_T14

description: SAMPLE 9


title: genomic DNA from UMSCC47 with Aza/TSA, UMSCC47_9_AzaTSA

description: SAMPLE 21

value: head and neck cancer


title: genomic DNA from OPSCC sample, MPC_T31

description: SAMPLE 17


title: genomic DNA from UMSCC47 without Aza/TSA, UMSCC47_1_DMSO

description: SAMPLE 20


title: genomic DNA from OPSCC sample, MPC_T23

description: SAMPLE 16


title: genomic DNA from OPSCC sample, MPC_T16

description: SAMPLE 11


title: ChIP-seq of GFP-tagged ZNF582 in HEK293 cells [ZNF582_rep1]


title: genomic DNA from OPSCC sample, MPC_T20

description: SAMPLE 14


title: genomic DNA from non-cancerous mucosa sample, MPC_N20

description: SAMPLE 4

value: oropharyngeal non-cancerous mucosa

value: normal


title: genomic DNA from OPSCC sample, MPC_T13

description: SAMPLE 8


title: ChIP-seq of GFP-tagged ZNF582 in HEK293 cells [ZNF582_rep2]


title: genomic DNA from OPSCC sample, MPC_T22

description: SAMPLE 15


title: genomic DNA from OPSCC sample, MPC_T19

description: SAMPLE 13


title: ChIP-seq of GFP-tagged ZIM3 in HEK293 cells [ZIM3_rep1]


title: genomic DNA from FaDu with Aza/TSA, FaDu_AzaTSA

description: SAMPLE 19

value: FaDu


title: genomic DNA from non-cancerous mucosa sample, MPC_N12

description: SAMPLE 2


title: genomic DNA from OPSCC sample, MPC_T17

description: SAMPLE 12


title: genomic DNA from FaDu without Aza/TSA, FaDu_DMSO

description: SAMPLE 18


title: genomic DNA from non-cancerous mucosa sample, MPC_N02

description: SAMPLE 1


title: ChIP-seq of GFP-tagged ZNF596 in HEK293 cells [ZNF596_rep2]


title: genomic DNA from OPSCC sample, MPC_T05

description: SAMPLE 6


title: genomic DNA from OPSCC sample, MPC_T06

description: SAMPLE 7


title: genomic DNA from OPSCC sample, MPC_T03

description: SAMPLE 5


title: genomic DNA from non-cancerous mucosa sample, MPC_N18

description: SAMPLE 3


title: ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep5]


title: ChIP-seq of GFP-tagged ZNF30 in HEK293 cells [ZNF30_rep2]


title: ChIP-seq of GFP-tagged ZNF30 in HEK293 cells [ZNF30_rep1]


title: ChIP-seq of GFP-tagged ZNF260 in HEK293 cells [ZNF260_rep1]


title: ChIP-seq of GFP-tagged ZFP28 in HEK293 cells [ZFP28_rep1]


title: ChIP-seq of GFP-tagged ZNF35 in HEK293 cells [ZNF35_rep2]


title: ChIP-seq of GFP-tagged ZNF250 in HEK293 cells [ZNF250_rep2]


title: ChIP-seq of GFP-tagged SNAI1 in HEK293 cells [SNAI1_rep2]


title: ChIP-seq of GFP-tagged ZNF121 in HEK293 cells [ZNF121_rep2]


title: ChIP-seq of GFP-tagged ZNF280A in HEK293 cells [ZNF280A_rep1]


title: ChIP-seq of GFP-tagged ZNF454 in HEK293 cells [ZNF454_rep2]


title: AdHBV_48hr_2

status: Public on Jan 20 2016

city: Philadelphia

first: James

middle: M

last: Wilson

state: Pennsylvania

address: 125S 31st St

institute: University of Pennsylvania

data_processing:
Sequencing and base calling were done using an Illumina NextSeq following standard methods by Drexel University College of Medicine Center for Genomic Sciences (1x75bp reads)
Reads were aligned to a reference genome consisting of the Rn5 build of the rat genome, the HBV serotype ayw sequence, the hrGFP sequence, and the pAdEasy1 sequence using the STAR aligner (v2.4.0h) using the options --outSAMtype BAM SortedByCoordinate and --outFilterMismatchNoverLmax 0.05
Mapped reads were filtered for "mapping quality = 255" using Sambamba (v0.4.7)
Reads per kilobase feature per megabase of library (RPKM) was calculated by counting reads per feature using the GenomicAlignments package (v1.2.1) in R (v3.1.2) and dividing these counts by kilobase of feature length to get RPK, then dividing by millions of reads per sample to get RPKM.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Tab-delimited with header.  Each row has counts/rpkm for all samples of each gene feature in the Rn5 GTF annotation  (named in first row).

organism: Rattus norvegicus

source_name: Cultured Primary Hepatocytes

growth_protocol: Primary rat hepatocytes were isolated using a 2-step perfusion protocol (Seglen, P. 1993. Methods Toxicol.) and plated on collagen coated 6cm plates.  Cells were maintained in Williams E Medium supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 4 μg/ml insulin-transferrin-selenium, 5 μg/ml hydrocortisone, and 5 ng/ml epidermal growth factor at 37°C in 5% CO2. Medium was changed on cells daily.

extract_protocol:
Total RNA was isolated using the mirVana RNA isolation kit following the manufacturer's total RNA isolation protocol.  Prior to cDNA library prep RNA was polyA selected
Libraries were prepared the sequencing facility of the Drexel University College of Medicine Center for Genomic Sciences using the Illumina TruSeq Stranded mRNA prep kit

treatment_protocol: Cells were left uninfected over 72hr or were infected with either AdGFP or AdHBV 24h after isolation and plating.  24h or 48h post-infection cells were washed with 1X PBS and stored at -80° until RNA isolation

value: hepatocyte

value: Sprague-Dawley

tag: treatment

value: AdHBV-infected

tag: collection time

value: 48h post-plating/24h post-infect


title: AdHBV_48hr_1


title: ChIP-seq of GFP-tagged ZNF322 in HEK293 cells [ZNF322_rep2]


title: AdGFP_48hr_2

value: AdGFP-infected


title: ChIP-seq of GFP-tagged ZNF140 in HEK293 cells [ZNF140_rep1]


title: AdGFP_48hr_3


title: ChIP-seq of GFP-tagged ZNF770 in HEK293 cells [ZNF770_rep1]


title: Uninfect_72hr_3

value: Uninfected

value: 72h post-plating


title: ChIP-seq of GFP-tagged ZNF146 in HEK293 cells [ZNF146_rep1]


title: Uninfect_48hr_3

value: 48h post-plating


title: ChIP-seq of GFP-tagged ZNF121 in HEK293 cells [ZNF121_rep1]


title: Uninfect_0hr_3

value: Freshly isolated/unplated


title: ChIP-seq of GFP-tagged ZNF134 in HEK293 cells [ZNF134_rep1]


title: Uninfect_0hr_1


title: ChIP-seq of GFP-tagged ZNF30 in HEK293 cells [ZNF30_rep3]


title: ChIP-seq of GFP-tagged ZNF8 in HEK293 cells [ZNF8_rep1]


title: hbv_48_3

status: Public on Jan 15 2016

data_processing:
Sequencing and base calling were done using an Illumina HiSeq following standard methods by GENEWIZ, Inc. (1x50bp reads) or with an Illumina NextSeq 500 instrument at the Drexel University College of Medicine Center for Genomic Sciences (1x75bp reads)
Reads were aligned to a reference genome consisting of the Rn5 build of the rat genome, the HBV serotype ayw sequence, the hrGFP sequence, and the pAdEasy1 sequence using the STAR aligner (v2.4.0h) using the options --outSAMtype BAM SortedByCoordinate and --outFilterMismatchNoverLmax 0.05
Mapped reads were filtered for "mapping quality = 255" using Sambamba (v0.4.7)
Reads per kilobase feature per megabase of library (RPKM) was calculated by counting reads per feature using the GenomicAlignments package (v1.2.1) in R (v3.1.2) and dividing these counts by kilobase of feature length to get RPK, then dividing by millions of reads per sample to get RPKM.
genome build: Rnor_5.0
processed data files format and content: Tab-delimited with header.  Each row has counts/rpkm for all 12 samples from merged BAM files) of each gene feature in the Rn5 GTF annotation  (named in first row).

extract_protocol:
Total RNA was isolated using the mirVana RNA isolation kit following the manufacturer's total RNA isolation protocol.  Prior to cDNA library prep RNA was polyA selected
Libraries were prepared by GENEWIZ, Inc. using the NEBNext Ultra RNA Library Prep following the manufacturer's protocol.

treatment_protocol: Cells were infected with either AdGFP or AdHBV 24h after isolation and plating.  24h or 48h post-infection cells were washed with 1X PBS and stored at -80° until RNA isolation

value: hepatocytes

value: 48h post-infection/72h post-plating


title: hbv_48_1


title: gfp_48_2


title: gfp_48_1


title: ChIP-seq of GFP-tagged ZNF708 in HEK293 cells [ZNF708_rep1]


title: ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep1]


title: ChIP-seq of GFP-tagged ZNF22 in HEK293 cells [ZNF22_rep4]


title: ChIP-seq of GFP-tagged SNAI1 in HEK293 cells [SNAI1_rep1]


title: ChIP-seq of GFP-tagged GLI4 in HEK293 cells [GLI4_rep1]


title: ChIP-seq of GFP-tagged ZNF18 in HEK293 cells [ZNF18_rep1]


title: hbv_24_3

value: 24h post-infection/48h post-plating


title: gfp_48_3


title: ChIP-seq of GFP-tagged ZNF264 in HEK293 cells [ZNF264_rep1]


title: AdHBV_72hr_3

value: 72h post-plating/48h post-infection


title: AdHBV_72hr_2


title: AdHBV_72hr_1


title: hbv_24_1


title: gfp_24_3


title: AdGFP_72hr_1


title: AdGFP_72hr_3


title: AdHBV_48hr_3


title: AdGFP_48hr_1


title: AdGFP_72hr_2


title: HL1cm-PC

status: Public on Aug 06 2015

city: Minneapolis

first: Brenda

last: Ogle

state: Minnesota

address: 312 Church St SE

department: Biomedical Engineering

institute: University of Minnesota-Twin Cities

description: total RNA

data_processing:
Gene expression analysis was performed with Galaxy software (Minnesota Supercomputing Institute (MSI), University of Minnesota, Minneapolis, MN).
Reads were processed and aligned to the mouse reference genome (mm10_genes_2012_05_23.gtf and canonical_mm10.fa) using Tophat (version 2.0.12, open source software, http://ccb.jhu.edu/software/tophat/index.shtml). The default options supplied with the software were used and the aligned read files produced by Tophat were processed using Cufflinks software (version 2.2.1, open source software, http://cole-trapnell-lab.github.io/cufflinks/).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file includes FPKM values for each Sample

source_name: HL-1 Cardiomyocyte, population control

growth_protocol: MSCs were cultured on a 0.1% gelatin (Sigma Aldrich, St. Louis, MO) pretreated flask containing a-minimum essential medium (MEM) complete. Alpha-MEM-complete consisted of a-MEM (Invitrogen, Carlsbad, CA), 10% fetal bovine serum (Hyclone, Logan, UT), 0.1 mM nonessential amino acids (Invitrogen), and 2 mM L-glutamine (Invitrogren).  MSC cultures were allowed to grow to 60-70% confluence and were replated at a concentration of 1,500 cells/cm2. HL1cms were cultured on fibronectin/gelatin (1.25 mg fibronectin/100 mL 0.02% gelatin) (Sigma Aldrich) pretreated flasks containing Claycomb-complete.  Claycomb-complete medium was comprised of Claycomb medium (SAFC Biosciences, St. Louis, MO, USA), 10% fetal bovine serum qualified for CMs (SAFC Biosciences), 100 U/mL: 100 μg/mL penicillin-streptomycin (Lonza, Walkersville, MD, USA), 0.1 mM norepinephrine (Sigma-Aldrich), and 2 mM L-glutamine (Invitrogen).  HL1cms were passaged at 100% confluence and split 1:3.

extract_protocol:
mMSCs were trypsinized from culture and placed into the Fluidigm C1 chip (17-25 micron) for capture.  HL1cm controls were captured in a similar manner. Population controls underwent same process as single cells but the samples contained the bulk population
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HL-1 cardiomyocyte, population control

tag: passages


title: HL1cm-4

description: total RNA of single-cell

source_name: HL-1 Cardiomyocyte

tag: cell type

value: HL-1 cardiomyocyte


title: mMSC14

description: total RNA of single-cell

source_name: Mouse bone marrow mesenchymal stem cell

value: Bone marrow MSC


title: Uninfect_72hr_1


title: Uninfect_72hr_2


title: Uninfect_24hr_2

value: 24h post-plating


title: Uninfect_48hr_1

value: hepatocyte


title: Uninfect_48hr_2

value: Sprague-Dawley


title: Uninfect_24hr_1


title: mMSC9

description: total RNA of single-cell


title: mMSC10

description: total RNA of single-cell


title: mMSC7

description: total RNA of single-cell


title: mMSC8

description: total RNA of single-cell


title: Uninfect_0hr_2


title: mMSC5

description: total RNA of single-cell


title: hbv_48_2

value: AdHBV-infected


title: mMSC2

description: total RNA of single-cell


title: mMSC1

description: total RNA of single-cell


title: hbv_24_2


title: gfp_24_2


title: gfp_24_1


title: HL1cm-5

description: total RNA of single-cell


title: HL1cm-3

description: total RNA of single-cell


title: mMSC-PC

description: total RNA

source_name: Mouse bone marrow mesenchymal stem cell, population control

value: Bone marrow MSC, population control


title: ChIP-seq of GFP-tagged ZNF454 in HEK293 cells

status: Public on Feb 17 2015

data_processing:
The 3’ end of reads were trimmed so that the final reads were 50 nucleotides long, and the reads were mapped to the human genome build GRCh37 using Bowtie 2 (29), with “--very-sensitive” preset of parameters. This parameter set allows one alignment to be reported for each read that is mapped to multiple positions on the genome, in addition to alignments of uniquely mappable reads. Duplicate reads, which often represent PCR amplification artifacts, were removed using SAMtools.
We performed two rounds of peak-calling: an initial round was performed without an explicit background model of read distributions, in order to identify ChIP experiments with similar experimental/read-mapping biases. We then constructed a background model for each sample, and repeated the peak-calling in order to identify the final set of protein-specific peaks. For the initial round, peaks were identified using MACS v1.4, with fragment length specified based on the results of cross-correlation analysis using SPP package (average 150 bp). Then, the overlap of the identified peaks for each pair of experiments was calculated as the total length of the intersection of peaks divided by the total length of the union of peaks from two experiments. Then, for each experiment x, the top 10 experiments with the highest overlap were identified, so that none of these 10 experiments would represent a biological replicate of experiment x. The reads from these 10 experiments were then randomly sampled, with probabilities proportional to the extent of overlap of each experiment with experiment x, so that a total of 5e+7 reads would be obtained. These reads were then used as the background model in order to perform a second, final round of peak-calling for experiment x, using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing peaks and peak summits

growth_protocol: HEK293 cells were cultured in Dulbecco's modified Eagle's medium with 10% fetal bovine serum and antibiotics. Gateway-compatible entry clones were cloned into the pDEST pcDNA5/FRT/TO-eGFP vector according to the manufacturer's instructions and co-transfected into Flp-In T-REx 293 cells together with the pOG44 Flp recombinase expression plasmid. Cells were selected for FRT site-specific recombination into the genome, following instructions by the manufacturer. Expression of the gene of interest was induced by addition of doxycycline to the culture medium 24 hours prior to harvesting.

extract_protocol:
HEK293 cells were cross-linked for 10 min in 1% formaldehyde. Lysates were sonicated to a DNA fragment length range of 200-300 bp using a Bioruptor (Diagenode). GFP-tagged transcription factors were immunoprecipitated with a polyclonal anti-GFP antibody (ab290, Abcam) and Dynabeads Protein G (Invitrogen). Subsequently, crosslinks were reversed at 65°C over night and bound DNA fragments were purified (EZ-10 Spin Column PCR Product Purification kit, Bio Basic).
Sequencing libraries were constructed using the NEBNext ChIP-Seq Library Prep kit (NEB) according the manufacturer's instructions.

tag: host cell line

tag: transfected with

value: GFP-tagged ZNF454

tag: chip antibody

value: polyclonal anti-GFP antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: ChIP-seq of GFP-tagged ZNF317 in HEK293 cells

value: GFP-tagged ZNF317


title: ChIP-seq of GFP-tagged ZNF416 in HEK293 cells

value: GFP-tagged ZNF416


title: ChIP-seq of GFP-tagged ZNF684 in HEK293 cells

value: GFP-tagged ZNF684


title: ChIP-seq of GFP-tagged ZIC2 in HEK293 cells

value: GFP-tagged ZIC2


title: HL1cm-1

description: total RNA of single-cell


title: ChIP-seq of GFP-tagged ZNF621 in HEK293 cells

value: GFP-tagged ZNF621


title: ChIP-seq of GFP-tagged ZNF692 in HEK293 cells

value: GFP-tagged ZNF692


title: ChIP-seq of GFP-tagged ZNF45 in HEK293 cells

value: GFP-tagged ZNF45


title: mMSC15

description: total RNA of single-cell


title: mMSC16

description: total RNA of single-cell


title: ChIP-seq of GFP-tagged ZNF136 in HEK293 cells

value: GFP-tagged ZNF136


title: ChIP-seq of GFP-tagged ZNF264 in HEK293 cells

value: GFP-tagged ZNF264


title: mMSC13

description: total RNA of single-cell

value: Bone marrow MSC


title: mMSC11

description: total RNA of single-cell


title: mMSC12

description: total RNA of single-cell


title: mMSC6

description: total RNA of single-cell


title: HL1cm-2

description: total RNA of single-cell

value: HL-1 cardiomyocyte


title: mMSC3

description: total RNA of single-cell


title: mMSC4

description: total RNA of single-cell


title: ChIP-seq of GFP-tagged ZNF16 in HEK293 cells

value: GFP-tagged ZNF16


title: ChIP-seq of GFP-tagged ZNF653 in HEK293 cells

value: GFP-tagged ZNF653


title: ChIP-seq of GFP-tagged ZNF41 in HEK293 cells

value: GFP-tagged ZNF41


title: ChIP-seq of GFP-tagged ZNF415 in HEK293 cells

value: GFP-tagged ZNF415


title: ChIP-seq of GFP-tagged ZNF33A in HEK293 cells

value: GFP-tagged ZNF33A

value: polyclonal anti-GFP antibody


title: ChIP-seq of GFP-tagged ZNF669 in HEK293 cells

value: GFP-tagged ZNF669

value: Abcam


title: ChIP-seq of GFP-tagged MZF1 in HEK293 cells

value: GFP-tagged MZF1


title: ChIP-seq of GFP-tagged ZNF528 in HEK293 cells

value: GFP-tagged ZNF528


title: ChIP-seq of GFP-tagged ZNF35 in HEK293 cells

value: GFP-tagged ZNF35


title: ChIP-seq of GFP-tagged ZNF382 in HEK293 cells

value: GFP-tagged ZNF382


title: ChIP-seq of GFP-tagged CTCF in HEK293 cells

value: GFP-tagged CTCF


title: ChIP-seq of GFP-tagged ZSCAN31 in HEK293 cells

value: GFP-tagged ZSCAN31


title: ChIP-seq of GFP-tagged ZSCAN22 in HEK293 cells

value: GFP-tagged ZSCAN22


title: ChIP-seq of GFP-tagged ZNF519 in HEK293 cells

value: GFP-tagged ZNF519


title: ChIP-seq of GFP-tagged ZNF322 in HEK293 cells

value: GFP-tagged ZNF322


title: ChIP-seq of GFP-tagged YY1 in HEK293 cells

value: GFP-tagged YY1


title: ChIP-seq of GFP-tagged ZNF71 in HEK293 cells

value: GFP-tagged ZNF71


title: ChIP-seq of GFP-tagged ZNF273 in HEK293 cells

value: GFP-tagged ZNF273


title: ChIP-seq of GFP-tagged ZFP3 in HEK293 cells

value: GFP-tagged ZFP3


title: ChIP-seq of GFP-tagged ZNF200 in HEK293 cells

value: GFP-tagged ZNF200


title: ChIP-seq of GFP-tagged ZNF467 in HEK293 cells

value: GFP-tagged ZNF467

value: polyclonal anti-GFP antibody


title: ChIP-seq of GFP-tagged KLF14 in HEK293 cells

value: GFP-tagged KLF14

value: Abcam