title: H_0695

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
mRNA-Seq reads were aligned against UCSC hg19 genome build with tophat 2.0.1, parameters --read-mismatches=3 --read-edit-dist=3 --max-multihits=20 --splice-mismatches=1 --microexon-search --coverage-search --mate-inner-dist=50 --mate-std-dev=50 –num-threads=8
Aligned reads were counted against the Gencode v17 gene annotation using htseq-count in the HTSeq package with –mode=intersection-nonempty
Genes were filtered from further analysis that had more than half of both HD and Control samples with zero counts
Outlier sample counts in individual genes were filtered
Differential expression between HD and Control was assessed using DESeq2 v1.3.34
Genome_build: hg19
Supplementary_files_format_and_content: processed files contain normalized counts for all samples and differential expression values from DESeq2, in tab delimited format

source_name: brain

extract_protocol:
QIAzol, Qiagen miRNeasy kit
Illumina TruSeq RNA Sample Prep Kit, mRNA

value: BA9 prefrontal cortex

tag: diagnosis

value: Huntington's Disease

tag: pmi

tag: age of death

tag: rin

tag: mrna-seq reads

tag: age of onset

tag: duration

tag: cag

tag: vonsattel grade

tag: h-v striatal score

tag: h-v cortical score


title: H_0726

status: Public on Dec 08 2015

type: SRA

city: Boston

state: MA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue


title: H_0700


title: H_0740


title: H_0681


title: EIH ID FG153

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

description: Saline Hyperthermic-EIH #16

data_processing:
Basecall files were converted to fastq files using CASAVA 1.8.2
Fastq files were clipped using fastq-mcf (parameters: “--max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25”)
Fastq files were aligned to rat Ensembl release 70 transcriptome (rn5) using bowtie 0.12.9 (params: “-e 500 –m 100 –chunkmbs 256”)
Alignments were quantified using RSEM v 1.2.0 (no special parameters)
Genome_build: Genome build: rn5
Supplementary_files_format_and_content: Separate count per gene files for each sample. A tab is between the gene and the count. One count per gene on each line.

molecule: total RNA

organism: Rattus norvegicus

source_name: Saline Hyperthermic-EIH

growth_protocol: Animals used in these experiments were Charles River male Sprague-Dawley. They were given access to water and food ad lib and kept on a 12 hour light cycle 6:00am to 6:00pm until testing

extract_protocol:
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).
Alpha and Beta Globin mRNA were substantially depleted from total RNA samples using the GlobinClear-Mouse/Rat Kit (Life Technologies # AM1981) as described by the vendor at EA/Quintiles; 4324 S. Alton Ave. Durham, N.C.  Analysis.
Globin mRNA-depleted RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Starting with 300 ng of Globin mRNA-depleted RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads.  Performed at EA/ Quintiles.
Final cDNA libraries were analyzed for size distribution and using an Agilent 2200 TapeStation, quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824) and normalized to 2 nM for sequencing. Performed at EA/Quintiles.
Clusters were generated on an Illumina cBOT using an Illumina TruSeq Paired-End Cluster Kit on an Illumina Paired End Flow Cell. The Flowcell was sequencing through 51 bases, paired end, (8 base index cycle) on an Illumina HiSeq 2000  (HiSeq Control Software v 1.5.15.1). Performed at EA/Quintiles.
Quality control files contained read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distribution of base quality and base frequency by sample.  Also, flow cell total yield, PF reads, barcode quality, alignment summaries and # of genes detected were determined.  FASTQ files for each RNA aliquot were generated.

treatment_protocol: Whole blood was obtained via cardiac puncture at 4:30 to 5:30 pm, and immediately frozen, from adult 85 to 90 day old male Sprague-Dawley rats at 3 hr after four sequential injections of saline, saline in a cool  environmental, saline in a hot envrionment (39°C), amphetamine or amphetamine in a cool environment

tag: strain

value: Sprague-Dawley

tag: age

value: adult

tag: gender

value: male

tag: sample group

value: Saline Hyperthermic-EIH

value: whole blood


title: EIH ID FG152

description: Saline Hyperthermic-EIH #15


title: H_0539


title: EIH ID FG100

description: Saline Hyperthermic-EIH #10


title: EIH ID FG101

description: Saline Hyperthermic-EIH #11


title: H_0010


title: H_0012


title: H_0009


title: EIH ID FG102

description: Saline Hyperthermic-EIH #12


title: H_0013


title: H_0750


title: H_0008


title: EIH ID FG97

description: Saline Hyperthermic-EIH #9


title: EIH ID FG95

description: Saline Hyperthermic-EIH #8


title: H_0007


title: EIH ID FG92

description: Saline Hyperthermic-EIH #7


title: H_0006


title: H_0005


title: WT sample 1

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1462

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

data_processing:
Basecalls by standard Illumina pipeline.
35~80 million 76 nucleotide pair-end reads were generated for each sample and aligned to the UCSC mm10 reference genome using tophat2 and bowtie2.
Transcript abundance, differential expression, and isoform quantitation were calculated using the cufflinks and cuffdiff suite from each pair of littermate samples or pooled control and mutant samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: sorted alveolar type 1 cells

extract_protocol:
Postnatal day 3 or 4 Scnn1a-Cre; RosamTmG/+ and Scnn1a-Cre; RosaSox2/+ littermate lungs were dissected in PBS. Around 3 mm wide strips were cut along the lobe edge, minced into pieces with forceps and digested in PBS with 2 mg/mL collagenase type I (Worthington,16 CLS-1) and 0.2 mg/mL DNase I (Worthington, D) for 40 min at 37 °C. An equal volume of 0.25% Trypsin/EDTA (Invitrogen, 25200-056) was added and incubated for another 10 min at 37 °C. Fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 5% and the tissue was triturated for 40~50 times. Dissociated cells were spun down at 6000 rpm for 1 min, resuspended in red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) for 3 min, washed with PBS with 1% FBS, SYTOX-red (Invitrogen, S34859) added to exclude dead cells and sorted on a BD Biosciences Influx sorter. RNA was extracted from at least 105 purified cells using Trizol reagents (Invitrogen, 15596018) and an RNeasy Micro kit (Qiagen, 74004).
100~200 ng total RNA was used to prepare an RNAseq library using an mRNA isolation kit (New England BioLabs, E7490) and a NEBNext Ultra RNA library prep kit (New England BioLabs, E7530S) with a final double (0.65 x -1 x bead volume) size selection step using a SPRIselect reagent kit (Beckman Coulter, B23318). Sequenced on an Illumina HiSeq2000.

value: mixed B6 and 129

tag: genotype

value: Scnn1a-Cre; Rosa[mTmG/+]


title: WT sample 2


title: H_0658

tag: diagnosis


title: Sox2 sample 2

value: Scnn1a-Cre; Rosa[Sox2/+]


title: Sox2 sample1


title: AMPH hot ID ML328

description: Amphetamine Hyperthermic #1

source_name: Amphetamine Hyperthermic

value: Amphetamine Hyperthermic


title: EIH ID FG91

description: Saline Hyperthermic-EIH #6


title: H_0003

tag: pmi


title: EIH ID FG90

description: Saline Hyperthermic-EIH #5


title: EIH ID FG138

description: Saline Hyperthermic-EIH #14


title: EIH ID FG137

description: Saline Hyperthermic-EIH #13


title: H_0002

tag: age of death


title: Mnase-dY-Tam-K4me1-rep1

city: San Francisco

first: Raga

last: Krishnakumar

state: CA

address: 912E RMB, 35 Medical Center Way

institute: UCSF

description: processed data file: MN-Tam-dY-K4me1.bw

library_source: genomic

data_processing:
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
ChromHMM was run on a subset of the data for identifying 6 chromatin states
MACS2 was used for peak finding using the following settings:
Dip-finding for nucleosome-free regions was performed as per: Wamstad, J. A., Alexander, J. M., Truty, R. M., Shrikumar, A., Li, F., Eilertson, K. E., et al. (2012). Cell, 151(1), 206–220. doi:10.1016/j.cell.2012.07.035
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for all ChIP-seq files - duplicates for Foxd3 conditional knockout data have been consolidated into one bigwig file

molecule: genomic DNA

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS (excpet EpiSCs, that were grown in a 50:50 mix of DMEM:glutamax and Neurobasal with N2 and B27 supplements), Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).

extract_protocol:
DNA was extracted using a standard ChIP protocol
Library was constructed using a standard Illumina protocol

treatment_protocol: Tamoxifen was added at 1uM for 36 hours to induce Foxd3 KO

tag: strain background

tag: genotype/variation

value: Foxd3 conditional knockout

tag: cell type

value: EpiC (dY cells)

tag: cell line of origin

value: epiblast cells:EpiC (dY cells)

tag: treatment

value: -Lif -2i day 3

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: Mnase-dY-Tam-K4me1-rep2

description: processed data file: MN-Tam-dY-K4me1.bw


title: Mnase-dY-EtOH-K4me1-rep2

description: processed data file: MN-EtOH-dY-K4me1.bw


title: Mnase-dY-EtOH-K4me1-rep1


title: EIH ID JB109

description: Saline Hyperthermic-EIH #3

tag: strain

tag: tissue


title: Mnase-R-Tam-K4me1-rep2

description: processed data file: MN-Tam-R-K4me1.bw

value: ESCs (R cells)

value: embryonic stem cells:ESCs (R cells)

value: Lif 2i


title: EIH ID JB110

description: Saline Hyperthermic-EIH #4

value: Sprague-Dawley

tag: age

tag: gender


title: Mnase-R-Tam-K4me1-rep1

description: processed data file: MN-Tam-R-K4me1.bw


title: EIH ID JB90

description: Saline Hyperthermic-EIH #2

value: adult

tag: sample group


title: Mnase-R-EtOH-K4me1-rep2

description: processed data file: MN-EtOH-R-K4me1.bw


title: Mnase-R-EtOH-K4me1-rep1

description: processed data file: MN-EtOH-R-K4me1.bw


title: H_0001

value: BA9 prefrontal cortex

tag: diagnosis

value: Huntington's Disease

tag: rin

tag: mrna-seq reads

tag: age of onset

tag: duration

tag: cag

tag: vonsattel grade

tag: h-v striatal score

tag: h-v cortical score


title: Mnase-dY-Tam-IgG

source_name: Mnase-dY-Tam-IgG

tag: strain background

tag: genotype/variation

tag: cell type

tag: cell line of origin

tag: treatment

tag: chip antibody

value: IgG (normal rabbit)

tag: chip antibody vendor

value: Invitrogen


title: EIH ID ML324

description: Saline Hyperthermic-EIH #1

tag: strain

tag: age

tag: gender

value: male

tag: sample group

value: Saline Hyperthermic-EIH

tag: tissue

value: whole blood


title: C_0083

tag: diagnosis

value: Neurologically normal

tag: pmi

tag: age of death

tag: rin

tag: mrna-seq reads


title: C_0082


title: dY-Tam-Brg1-rep2

description: processed data file: dY-Tam-BRG1.bw

tag: strain background

value: Foxd3 conditional knockout

value: EpiC (dY cells)

tag: chip antibody cat. #

tag: chip antibody lot #


title: Mnase-R-EtOH-IgG

source_name: Mnase-R-EtOH-IgG

tag: genotype/variation

tag: cell type

tag: cell line of origin


title: Control ID FG150

description: Saline Control #15

source_name: Saline Control

value: Saline Control


title: Mnase-R-Tam-IgG

source_name: Mnase-R-Tam-IgG

tag: treatment

tag: chip antibody

tag: chip antibody vendor


title: C_0077


title: Mnase-dY-EtOH-IgG

source_name: Mnase-dY-EtOH-IgG

value: epiblast cells:EpiC (dY cells)

value: -Lif -2i day 3


title: C_0081


title: dY-Tam-HDAC1-rep2

description: processed data file: dY-Tam-HDAC.bw

value: Abcam


title: Control ID FG136

description: Saline Control #14

tag: strain

tag: age

tag: gender


title: H_0657

tag: tissue

tag: diagnosis

tag: age of onset

tag: duration

tag: cag

tag: vonsattel grade

tag: h-v striatal score

tag: h-v cortical score


title: dY-Tam-Brg1-rep1

description: processed data file: dY-Tam-BRG1.bw

tag: strain background

tag: genotype/variation

tag: chip antibody cat. #

tag: chip antibody lot #


title: dY-Tam-HDAC1-rep1

description: processed data file: dY-Tam-HDAC.bw

tag: cell type

tag: cell line of origin

tag: treatment

tag: chip antibody


title: C_0076

tag: pmi

tag: age of death

tag: rin

tag: mrna-seq reads


title: Control ID FG135

description: Saline Control #13

tag: strain

tag: age

tag: gender

tag: sample group

tag: tissue


title: dY-Tam-IgG

source_name: dY-Tam-IgG

tag: strain background

tag: chip antibody vendor


title: C_0087

tag: diagnosis


title: C_0075


title: dY-EtOH-Brg1-rep2

description: processed data file: dY-EtOH-BRG1.bw

tag: genotype/variation

tag: chip antibody cat. #

tag: chip antibody lot #


title: Control ID FG131

description: Saline Control #12


title: dY-EtOH-HDAC1-rep2

description: processed data file: dY-EtOH-HDAC.bw

tag: cell type

tag: cell line of origin

tag: treatment


title: dY-EtOH-Brg1-rep1

description: processed data file: dY-EtOH-BRG1.bw

tag: chip antibody


title: Control ID FG151

description: Saline Control #16


title: Control ID FG130

description: Saline Control #11


title: dY-EtOH-IgG

source_name: dY-EtOH-IgG


title: C_0071

tag: pmi

tag: age of death

tag: rin


title: C_0070

tag: mrna-seq reads


title: Control ID FG99

description: Saline Control #10

tag: strain

tag: age

tag: gender


title: C_0069

tag: tissue


title: R-Tam-HDAC1-rep2

description: processed data file: R-Tam-HDAC.bw

tag: strain background

value: ESCs (R cells)

value: embryonic stem cells:ESCs (R cells)

value: Lif 2i

tag: chip antibody vendor


title: Control ID FG94

description: Saline Control #8

value: Sprague-Dawley

value: adult

tag: sample group


title: C_0065

value: BA9 prefrontal cortex

tag: diagnosis


title: R-Tam-HDAC1-rep1

description: processed data file: R-Tam-HDAC.bw

tag: genotype/variation

tag: chip antibody cat. #

tag: chip antibody lot #


title: R-Tam-Brg1-rep1

description: processed data file: R-Tam-BRG1.bw

tag: cell type

tag: cell line of origin

tag: treatment


title: R-Tam-IgG

source_name: R-Tam-IgG

tag: chip antibody

value: IgG (normal rabbit)

value: Invitrogen


title: R-EtOH-Brg1-rep2

description: processed data file: R-EtOH-BRG1.bw


title: C_0062

tag: pmi

tag: age of death

tag: rin


title: R-EtOH-Brg1-rep1

description: processed data file: R-EtOH-BRG1.bw


title: R-EtOH-HDAC1-rep2

description: processed data file: R-EtOH-HDAC.bw


title: Control ID FG93

description: Saline Control #7

tag: strain

tag: age

value: male


title: C_0061

tag: tissue

tag: mrna-seq reads


title: Control ID FG89

description: Saline Control #6

tag: gender

value: whole blood


title: R-EtOH-HDAC1-rep1

description: processed data file: R-EtOH-HDAC.bw

tag: strain background

tag: chip antibody vendor


title: C_0060

tag: diagnosis

value: Neurologically normal


title: dY-E2-Flag-rep3

tag: genotype/variation

value: Foxd3 conditional knockout targeted with 3XFlag tag into endogenous Foxd3 allele

value: M2 anti-Flag

value: Sigma

tag: chip antibody cat. #


title: Control ID FG88

description: Saline Control #5

tag: sample group

value: Saline Control


title: dY-EtOH-HDAC1-rep1

description: processed data file: dY-EtOH-HDAC.bw

value: Foxd3 conditional knockout

tag: cell type

value: EpiC (dY cells)

tag: cell line of origin

value: epiblast cells:EpiC (dY cells)

value: -Lif -2i day 3

tag: chip antibody lot #


title: dY-FCKO-Flag-rep3

source_name: dY-FCKO-Flag

tag: treatment

tag: chip antibody


title: C_0053

tag: pmi

tag: age of death

tag: rin


title: R-E2-Flag-rep3

value: ESCs (R cells)

value: embryonic stem cells:ESCs (R cells)

value: Lif 2i


title: Control ID FG98

description: Saline Control #9

tag: strain

value: Sprague-Dawley

tag: age

value: adult

tag: tissue


title: R-FCKO-Flag-rep3

source_name: R-FCKO-Flag

tag: strain background


title: dY-Foxd3CKO-Tam-H3K27me3 ChIP-rep2

description: processed data file: dYT-K27me3.bw

data_processing:
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
ChromHMM was run on a subset of the data for identifying 6 chromatin states
MACS2 was used for peak finding using the following settings:
Dip-finding for nucleosome-free regions was performed as per: Wamstad, J. A., Alexander, J. M., Truty, R. M., Shrikumar, A., Li, F., Eilertson, K. E., et al. (2012). Cell, 151(1), 206–220. doi:10.1016/j.cell.2012.07.035
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for all ChIP-seq files; duplicates for Foxd3 conditional knockout data have been consolidated into one bigwig file

source_name: dY-Foxd3CKO-Tam-H3K27me3 ChIP

value: EpiLC (dY cells); epiblast-like cells

value: Foxd3 conditional knockout C57BL/6 ESCs

tag: chip antibody vendor

value: Millipore


title: dY-Foxd3CKO-Tam-H3K27ac ChIP-rep2

description: processed data file: dYT-K27a.bw

source_name: dY-Foxd3CKO-Tam-H3K27ac ChIP

value: Active Motif


title: dY-Foxd3CKO-Tam-H3K4me3 ChIP-rep2

description: processed data file: dYT-K4me3.bw

source_name: dY-Foxd3CKO-Tam-H3K4me3 ChIP

value: Abcam


title: dY-Foxd3CKO-Tam-H3K4me1 ChIP-rep2

description: processed data file: dYT-K4me1.bw

source_name: dY-Foxd3CKO-Tam-H3K4me1 ChIP


title: R-Tam-Brg1-rep2

description: processed data file: R-Tam-BRG1.bw


title: Control ID JB88

description: Saline Control #2

tag: gender

value: male

value: whole blood


title: Control ID ML322

description: Saline Control #1

value: Saline Control


title: C_0038

source_name: brain

value: BA9 prefrontal cortex

tag: diagnosis

value: Neurologically normal

tag: mrna-seq reads


title: Control ID FG82

description: Saline Control #4

tag: sample group


title: Control ID JB108

description: Saline Control #3


title: C_0037


title: dY-Foxd3CKO-Tam-p300 ChIP-rep1

description: processed data file: dYT-p300.bw

source_name: dY-Foxd3CKO-Tam-p300 ChIP

tag: genotype/variation

value: Foxd3 conditional knockout

tag: cell type

value: Santa Cruz

tag: chip antibody cat. #


title: dY-Foxd3CKO-Tam-IgG ChIP-rep2

description: processed data file: dYT-IgG.bw

source_name: dY-Foxd3CKO-Tam-IgG ChIP

tag: cell line of origin

tag: treatment

value: -Lif -2i day 3

value: IgG (normal rabbit)

value: Invitrogen

tag: chip antibody lot #


title: C_0036

tag: pmi

tag: age of death


title: dY-Foxd3CKO-Tam-H3K27ac ChIP-rep1

description: processed data file: dYT-K27a.bw

tag: chip antibody


title: dY-Foxd3CKO-Tam-H3K4me3 ChIP-rep1

description: processed data file: dYT-K4me3.bw


title: dY-Foxd3CKO-Tam-H3K4me1 ChIP-rep1

description: processed data file: dYT-K4me1.bw


title: R-EtOH-IgG

source_name: R-EtOH-IgG

value: ESCs (R cells)

value: embryonic stem cells:ESCs (R cells)

value: Lif 2i


title: dY-Foxd3CKO-Tam-IgG ChIP-rep1

description: processed data file: dYT-IgG.bw

value: EpiLC (dY cells); epiblast-like cells

value: Foxd3 conditional knockout C57BL/6 ESCs


title: C_0033

tag: rin


title: C_0035

tag: tissue


title: dY-Foxd3CKO-Tam-p300 ChIP-rep2

description: processed data file: dYT-p300.bw

tag: strain background


title: C_0050


title: dY-Foxd3CKO-EtOH-H3K27ac ChIP-rep2

description: processed data file: dYE-K27a.bw

source_name: dY-Foxd3CKO-EtOH-H3K27ac ChIP

tag: chip antibody vendor

value: Active Motif


title: C_0032


title: dY-Foxd3CKO-EtOH-H3K27me3 ChIP-rep2

description: processed data file: dYE-K27me3.bw

source_name: dY-Foxd3CKO-EtOH-H3K27me3 ChIP

value: Millipore


title: dY-Foxd3CKO-EtOH-H3K4me3 ChIP-rep2

description: processed data file: dYE-K4me3.bw

source_name: dY-Foxd3CKO-EtOH-H3K4me3 ChIP

value: Abcam


title: C_0031


title: C_0039


title: dY-Foxd3CKO-EtOH-H3K4me1 ChIP-rep2

description: processed data file: dYE-K4me1.bw

source_name: dY-Foxd3CKO-EtOH-H3K4me1 ChIP


title: dY-Foxd3CKO-EtOH-p300 ChIP-rep1

description: processed data file: dYE-p300.bw

source_name: dY-Foxd3CKO-EtOH-p300 ChIP


title: dY-Foxd3CKO-Tam-H3K27me3 ChIP-rep1

description: processed data file: dYT-K27me3.bw


title: dY-Foxd3CKO-EtOH-H3K27ac ChIP-rep1

description: processed data file: dYE-K27a.bw


title: C_0029


title: C_0026


title: dY-Foxd3CKO-EtOH-H3K4me1 ChIP-rep1

description: processed data file: dYE-K4me1.bw


title: dY-Foxd3CKO-EtOH-IgG ChIP-rep2

description: processed data file: dYE-IgG.bw

source_name: dY-Foxd3CKO-EtOH-IgG ChIP


title: dY-Foxd3CKO-EtOH-IgG ChIP-rep1

description: processed data file: dYE-IgG.bw


title: C_0024


title: C_0025


title: dY-Foxd3CKO-EtOH-H3K4me3 ChIP-rep1

description: processed data file: dYE-K4me3.bw


title: dY-Foxd3CKO-EtOH-H3K27me3 ChIP-rep1

description: processed data file: dYE-K27me3.bw


title: M2_input ATAC Seq

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

description: accessible chromatin

data_processing:
Library strategy: ATAC-Seq
Alignment - BWA 0.7.2
Strip mitochondrial reads/Sort (samtools 0.1.18)
Deduplicate Reads (Picard 1.9.1 MarkDuplicates)
Call Peaks (MACS2.0.10 default settings plus -q 0.05)
Genome_build: HG19
Supplementary_files_format_and_content: Encode Format NarrowPeak files for each Sample. The narrowPeak files were generated with input samples using MACS2 with    settings described above; column 7 is the fold change    over local background.

source_name: GBM primary culture G514NS

growth_protocol: Cells derived from an adult GBM patient and mantained in neural stem-like conditions according to a paper by Pollard et al (2009) Cell Stem Cell.

extract_protocol:
ATAC was performed on 50,000 cells with Nextera® DNA Sample Preparation Kit (FC-121-1030, Illumina). In parallel, 50,000 cells from each biological replicate were used to extract total DNA that was later sequenced as input.
Library construction was performed as per manual of the Nextera® DNA Sample Preparation Kit (FC-121-1030, Illumina).

treatment_protocol: One million cells were transfected with plasmids for the expression of either EGFP or the N-terminal isoform of the ER. Plasmid backbone was pcDNA-DEST40. Three independent transfections were performed per construct.

tag: tumor

value: glioblastoma

tag: transfection construct

value: epigenetic regulator

tag: technique

value: ATAC

tag: developmental stage

value: adult


title: M3 ATAC Seq

description: accessible chromatin


title: dY-Foxd3CKO-EtOH-p300 ChIP-rep2

description: processed data file: dYE-p300.bw

tag: genotype/variation

value: Foxd3 conditional knockout


title: C_0023

value: BA9 prefrontal cortex

tag: diagnosis

value: Neurologically normal

tag: mrna-seq reads


title: R-Foxd3CKO-Tam-H3K27me3 ChIP-rep2

description: processed data file: RT-K27me3.bw

source_name: R-Foxd3CKO-Tam-H3K27me3 ChIP

tag: cell type

value: embryonic stem cells (ESCs; R cells)

tag: cell line of origin

tag: chip antibody cat. #


title: M2 ATAC Seq

description: accessible chromatin


title: R-Foxd3CKO-Tam-p300 ChIP-rep2

description: processed data file: RT-p300.bw

source_name: R-Foxd3CKO-Tam-p300 ChIP

tag: treatment

value: Santa Cruz

tag: chip antibody lot #


title: M1_input ATAC Seq

description: accessible chromatin


title: R-Foxd3CKO-Tam-p300 ChIP-rep1

description: processed data file: RT-p300.bw

tag: chip antibody


title: R-Foxd3CKO-Tam-H3K27ac ChIP-rep2

description: processed data file: RT-K27a.bw

source_name: R-Foxd3CKO-Tam-H3K27ac ChIP


title: C_0021

tag: pmi

tag: age of death

tag: rin


title: R-Foxd3CKO-Tam-IgG ChIP-rep2

description: processed data file: RT-IgG.bw

source_name: R-Foxd3CKO-Tam-IgG ChIP

tag: strain background

value: IgG (normal rabbit)

tag: chip antibody vendor

value: Invitrogen


title: R-Foxd3CKO-Tam-H3K4me1 ChIP-rep2

description: processed data file: RT-K4me1.bw

source_name: R-Foxd3CKO-Tam-H3K4me1 ChIP

value: Lif 2i


title: R-Foxd3CKO-Tam-H3K27me3 ChIP-rep1

description: processed data file: RT-K27me3.bw


title: C_0022

tag: tissue


title: R-Foxd3CKO-Tam-H3K4me3 ChIP-rep2

description: processed data file: RT-K4me3.bw

source_name: R-Foxd3CKO-Tam-H3K4me3 ChIP


title: M3_input ATAC Seq

description: accessible chromatin

tag: tumor

tag: transfection construct

tag: technique


title: R-Foxd3CKO-Tam-H3K27ac ChIP-rep1

description: processed data file: RT-K27a.bw

tag: genotype/variation


title: M1 ATAC Seq

description: accessible chromatin

tag: developmental stage


title: C_0020

source_name: brain

tag: diagnosis

tag: mrna-seq reads


title: R-Foxd3CKO-Tam-H3K4me3 ChIP-rep1

description: processed data file: RT-K4me3.bw

tag: cell type

tag: cell line of origin

tag: chip antibody cat. #


title: E3_input ATAC Seq

description: accessible chromatin

value: EGFP


title: R-Foxd3CKO-Tam-H3K4me1 ChIP-rep1

description: processed data file: RT-K4me1.bw

value: Foxd3 conditional knockout C57BL/6 ESCs

tag: treatment

tag: chip antibody

tag: chip antibody lot #


title: C_0019

tag: pmi

tag: age of death

tag: rin


title: C_0018

tag: tissue


title: E3 ATAC Seq

description: accessible chromatin

tag: tumor


title: R-Foxd3CKO-EtOH-p300 ChIP-rep2

description: processed data file: RE-p300.bw

source_name: R-Foxd3CKO-EtOH-p300 ChIP

tag: strain background

tag: chip antibody vendor


title: C_0017


title: R-Foxd3CKO-EtOH-H3K27me3 ChIP-rep2

description: processed data file: RE-K27me3.bw

source_name: R-Foxd3CKO-EtOH-H3K27me3 ChIP

tag: genotype/variation


title: E2_input ATAC Seq

description: accessible chromatin

tag: transfection construct

tag: technique

tag: developmental stage


title: R-Foxd3CKO-EtOH-H3K27ac ChIP-rep2

description: processed data file: RE-K27a.bw

source_name: R-Foxd3CKO-EtOH-H3K27ac ChIP

tag: cell type

value: Active Motif


title: R-Foxd3CKO-EtOH-H3K4me3 ChIP-rep2

description: processed data file: RE-K4me3.bw

source_name: R-Foxd3CKO-EtOH-H3K4me3 ChIP

tag: cell line of origin


title: C_0016

tag: diagnosis

tag: mrna-seq reads


title: R-Foxd3CKO-EtOH-p300 ChIP-rep1

description: processed data file: RE-p300.bw

tag: treatment

tag: chip antibody

tag: chip antibody cat. #


title: E2 ATAC Seq

description: accessible chromatin


title: R-Foxd3CKO-EtOH-H3K4me1 ChIP-rep2

description: processed data file: RE-K4me1.bw

source_name: R-Foxd3CKO-EtOH-H3K4me1 ChIP

tag: chip antibody lot #


title: R-Foxd3CKO-EtOH-IgG ChIP-rep2

description: processed data file: RE-IgG.bw

source_name: R-Foxd3CKO-EtOH-IgG ChIP


title: E1_input_ATAC Seq

description: accessible chromatin


title: E1 ATAC Seq

description: accessible chromatin


title: R-Foxd3CKO-EtOH-H3K27me3 ChIP-rep1

description: processed data file: RE-K27me3.bw

value: Millipore


title: R-Foxd3CKO-EtOH-H3K4me1 ChIP-rep1

description: processed data file: RE-K4me1.bw

value: Abcam


title: R-Foxd3CKO-EtOH-H3K27ac ChIP-rep1

description: processed data file: RE-K27a.bw


title: C_0014

tag: pmi

tag: age of death

tag: rin


title: C_0015

tag: tissue


title: R-Foxd3CKO-Tam-IgG ChIP-rep1

description: processed data file: RT-IgG.bw

tag: strain background

tag: chip antibody vendor


title: R-Foxd3CKO-EtOH-H3K4me3 ChIP-rep1

description: processed data file: RE-K4me3.bw

tag: genotype/variation


title: C_0013


title: C_0011


title: R-Foxd3CKO-EtOH-IgG ChIP-rep1

description: processed data file: RE-IgG.bw


title: dY-Targ-Flag ChIP-rep1

source_name: dY-Targ-Flag ChIP

value: Foxd3 conditional knockout with 3XFlag tag into endogenous Foxd3 allele

value: EpiLC (dY cells); epiblast-like cells

value: Foxd3 conditional knockout C57BL/6 ESCs targeted with 3XFlag tag into endogenous Foxd3 allele

value: M2 anti-Flag

value: Sigma


title: dY-Targ-Flag ChIP-rep2


title: dY-Ctrl-Flag ChIP-rep2

source_name: dY-Ctrl-Flag ChIP

value: Foxd3 conditional knockout


title: C_0012

value: BA9 prefrontal cortex

value: Neurologically normal


title: R-Targ-Flag ChIP-rep2

source_name: R-Targ-Flag ChIP

value: embryonic stem cells (ESCs; R cells)


title: C_0006


title: dY-Ctrl-Flag ChIP-rep1


title: C_0005


title: C_0004


title: R-Targ-Flag ChIP-rep1


title: R-Ctrl-Flag ChIP-rep2

source_name: R-Ctrl-Flag ChIP


title: R-Ctrl-Flag ChIP-rep1


title: G-p300 ChIP

source_name: G-p300 ChIP

value: EpiSCs (G cells); epiblast stem cells

value: dual miRNA reporter V6.5 ESCs

value: bFgf Activin

value: Santa Cruz


title: C_0002


title: G-H3K27me3 ChIP

source_name: G-H3K27me3 ChIP


title: C_0003


title: Dzip3_ChIPSeq

city: Nagasaki

first: Daishi

last: Inoue

address: Sakamoto

department: medicine

country: Japan

institute: Nagasaki univiersity

data_processing:
Basecalls performed using Illumina MiSeq
ChIP-seq reads were aligned to the mm9 genome assembly using Illumina MiSeq
Genome_build: mm9

growth_protocol: E14 mES cells were cultured in feeder-free conditions on 0.5% gelatin-coated dishes with 2i+LIF medium (N2B27 medium [Life Technologies], 1 µM PD0325901 and 3 µM CHIR99021 [STEMGENT], together known as 2i, and 1000 U/ml LIF)

extract_protocol:
mES cells cultured in 2i+LIF were collected, fixed for 10 min in 1% formaldehyde, and sheared using a Picoruptor.Histone-DNA complexes were isolated with antibody. Antibodies against Dzip3,  Ring1B and ubH2A  were prepared by immunizing rabbits in our laboratory.
ChIP-seq libraries were prepared from ChIP samples using the ChIP-Seq Sample Prep kit (Illumina).

tag: strain

value: embryonic stem cell

tag: passages

value: passage 3-5


title: ubH2A_ChIPSeq

tag: cell type


title: input DNA


title: Dzip3-KD rep2

data_processing:
Basecalls performed using Illumina MiSeq
RNA-seq reads were aligned to the mm9 genome assembly using Illumina MiSeq
Genome_build: mm9

extract_protocol:
mES cells cultured in 2i+LIF were collected.Total RNA was isolated using ISOGEN II reagent (NIPPON GENE), according to the manufacturer’s protocol. cDNA was created from 0.5 μg total RNA using an oligo(dT) primer (Life Technologies), random hexamers (TAKARA), and M-MuLV reverse transcriptase (NEB).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina)

value: Dzip3 knockdown


title: G-RNA Pol2 ChIP

description: sc-900X, lotG1511 and sc-899X, lot B2412 used at 4:1

source_name: G-RNA Pol2 ChIP

tag: cell line of origin

value: Pan-RNA Pol2


title: Ring1B_ChIPSeq


title: G-H3K27ac ChIP

source_name: G-H3K27ac ChIP

value: Active Motif


title: G-H3K4me3 ChIP

source_name: G-H3K4me3 ChIP

value: Abcam


title: C_0010

tag: diagnosis


title: C_0008

tag: mrna-seq reads


title: dY-RNA Pol2 ChIP

source_name: dY-RNA Pol2 ChIP

value: EpiLC (dY cells); epiblast-like cells

tag: treatment

value: -Lif -2i day 3


title: Dzip3-KD rep1


title: G-IgG ChIP

source_name: G-IgG ChIP

tag: chip antibody

value: IgG (normal rabbit)

value: Invitrogen


title: Ring1B-KD rep2

value: Ring1B knockdown


title: Ring1B-KD rep1


title: C_0009

source_name: brain

value: BA9 prefrontal cortex

value: Neurologically normal


title: control rep2

value: wild type


title: control rep1


title: dY-Oct4 ChIP

source_name: dY-Oct4 ChIP

value: dual miRNA reporter V6.5 ESCs

tag: chip antibody cat. #


title: dY-p300 ChIP

source_name: dY-p300 ChIP

tag: chip antibody lot #


title: dY-H3K27me3 ChIP

source_name: dY-H3K27me3 ChIP

value: Millipore


title: dY-H3K27ac ChIP

source_name: dY-H3K27ac ChIP


title: dY-IgG ChIP

source_name: dY-IgG ChIP


title: dR-RNA Pol2 ChIP

source_name: dR-RNA Pol2 ChIP

value: day 1 ESC differentiation (dR cells)

value: -Lif -2i day 1

value: Santa Cruz


title: G-H3K4me1 ChIP

source_name: G-H3K4me1 ChIP

value: EpiSCs (G cells); epiblast stem cells

value: bFgf Activin


title: dR-p300 ChIP

source_name: dR-p300 ChIP


title: dR-H3K27me3 ChIP

source_name: dR-H3K27me3 ChIP


title: dR-Oct4 ChIP

source_name: dR-Oct4 ChIP


title: dY-H3K4me1 ChIP

source_name: dY-H3K4me1 ChIP


title: dR-H3K27ac ChIP

source_name: dR-H3K27ac ChIP

value: Active Motif


title: dR-H3K4me3 ChIP

source_name: dR-H3K4me3 ChIP

value: Abcam


title: dR-H3K4me1 ChIP

source_name: dR-H3K4me1 ChIP


title: dR-IgG ChIP

source_name: dR-IgG ChIP


title: R-RNA Pol2 ChIP

source_name: R-RNA Pol2 ChIP

value: embryonic stem cells (ESCs; R cells)

value: Lif 2i

value: Pan-RNA Pol2


title: R-Oct4 ChIP

source_name: R-Oct4 ChIP


title: R-p300 ChIP

source_name: R-p300 ChIP


title: TDRD6 KnockOut (Tdrd6-/-) 2

city: Dresden

first: Rolf

last: Jessberger

state: Saxony

address: Fetscherstraße 74

department: Institut für Physiologische Chemie

country: Germany

institute: Technische Universität Dresden

data_processing:
alignment against mm9 with tophat 2.0.9 and bowtie2 2.10
gtf with isoforms was built using cuffcompare, mm9 and Ensembl 67 gtf file
Cufflinks Version 2.1.1 was used for the transcript expression analysis. It was run on the 8 samples which are included in this record.
The command call was the following: cuffdiff -o allsamples -L HET,KO -p 6  --compatible-hits-norm -b /projects/seq-work/user/all/reference/mus_musculus/mm9/mm9.fa -u -M transcripts.not.used.gtf --FDR 0.1 --library-type fr-firststrand --library-norm-method geometric --dispersion-method pooled cuffcmp-Ensembl67/cuffcmp.combined.gtf het1.bam, het2.bam, het3.bam, het4.bam ko1.bam,ko2.bam,ko3.bam,ko4.bam.
Afterwards the results were filtered for transcripts having a certain 3' UTR length. The UTR length was extracted from Ensembl via (http://www.ensembl.org/biomart). These transcripts were split up into 3 spreadsheets which are in the excel workbook. The first spreadsheet contains information for transcripts with 3' UTR length less than 350 nt. The second spreadsheet contains information for transcripts with 3' UTR length between 350 and 1500 nt. The third spreadsheet contains information for transcripts with 3' UTR length more than 1500 nt. Each spreadsheet contains 12 columns with information regarding the transcripts. First column contains the gene/transcript ID from the Cufflinks/Cuffdiff call. Second column contains the official gene name and the third column the loci of the transcript on the reference. 4th columns contains the first sample name and correspond with the value of the transcript (of the same row) in first sample expressed as FPKM in 6h column. 5th column contains the second sample name and correspond with the value of the transcript (of the same row) in second sample expressed as FPKM in 7th column. Eighth column contains the log 2 fold change between values in the column six and column seven. 9th column contains the value of the test statistic used to compute significance of the observed change in FPKM. 10th column shows the uncorrected p-value of the test statistic and the 11th column the FDR-adjusted p-value of the test statistic. Last column has the transcript ID from Ensembl
Genome_build: mm9
Supplementary_files_format_and_content: the expression of transcripts, an output from cufflinks with transcripts of interest and columns which didn't provide information for the analysis have been removed

source_name: TDRD6 Knockout_round spermatids

growth_protocol: Animals were bred and maintained under pathogen-free conditions at the Experimental Center of the Medizinisch-Theoretisches Zentrum of the Medical Faculty at the Dresden University of Technology according to approved animal welfare guidelines

extract_protocol:
Total RNA was extracted using the TRIZOL Reagent (Invitrogen), according to the manufacturer’s instructions.
Poly-dT enrichment of mRNA, standard workflow of NEBNext® Ultra Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Testes from postnatal day 26 (P26) Tdrd6+/- and Tdrd6-/- mice were dissected to be enriched in round spermatid cells. Construction of TDRD6‐deficient mice was described previously (Vasileva, Tiedau et al. 2009). Tdrd6+/- mice used as control for the experiments do not exhibit any phenotype and provide the targeting vector with the hCD4 gene in frame with the Tdrd6 5′ UTR and ATG (start) codon, that allows isolation of TDRD6 expressing cells through an anti hCD4-MACS approach (Vasileva, Tiedau et al. 2009). For cell preparations enriched in round spermatids, the Tunica albuginea was removed and seminiferous tubules resuspended in 10 ml PBS and passed subsequently through 100μm and 40μm stainers. Cells were washed once with PBS and hCD4-positive cells were magnetically labeled with CD4MicroBeads (Miltenyi Biotec) and MACS isolated (Miltenyi Biotec) according to manufacturer instructions.

value: TDRD6 KnockOut (Tdrd6-/-)

tag: age

value: postnatal date 26 (P26)

value: testis

tag: developmental stage

value: post meiotic cells

value: round spermatids


title: TDRD6 Heterozygote (Tdrd6+/-) 1

source_name: TDRD6 heterozygote_round spermatids

value: TDRD6 Heterozygote (Tdrd6+/-)


title: TDRD6 KnockOut (Tdrd6-/-) 3


title: TDRD6 Heterozygote (Tdrd6+/-) 2


title: TDRD6 Heterozygote (Tdrd6+/-) 3


title: TDRD6 KnockOut (Tdrd6-/-) 4


title: dY-H3K4me3 ChIP

source_name: dY-H3K4me3 ChIP

value: EpiLC (dY cells); epiblast-like cells

value: dual miRNA reporter V6.5 ESCs

value: -Lif -2i day 3


title: R-H3K27me3 ChIP

source_name: R-H3K27me3 ChIP

value: Millipore


title: Immunostimulatory dendritic cells from LCMV-Cl13 infected mice

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

data_processing:
Sequence reads from each sample were trimmed to remove the adapter and barcode sequences and the resulting 75 bp reads were mapped to the GRCm38/mm10 mouse genome assembly
Alignment was done using Tophat (v.2.0.13). command: tophat --no-novel-juncs --library-type fr-unstranded -G Illumina_iGenomes_mm10_associated_genes.gtf
Read counts were obtained using HTSeq (v0.6.1) and only single-mapped reads were counted for analysis using the gene model file from the alignment step
RPKM values were calculated by dividing the read counts by gene length (in Kb) and the total number of single-mapped reads (in millions) for each sample
Only genes expressed at 2 RPKM or above were used for analysis
Genome_build: UCSC mm10, GRCm38
Supplementary_files_format_and_content: Tab-delimited file RPKM values for all genes

source_name: day 9 of a lymphocytic choriomeningitis virus clone 13 infected mouse

growth_protocol: Mice were 6-8 weeks old upon cell harvest

extract_protocol:
iregDCs and stimDCs (spleen) were FACSorted based on CD39 and CD95 expression nine days following LCMV-Cl13 infection. In parallel, naive monocytes (bone marrow) and cDCs (spleen) were FACSorted from naïve mice. Total RNA from each population was harvested using the RNeasy extraction kit (Qiagen), converted into double-stranded cDNA and amplified using the Ovation RNA-Seq System V2 (NuGEN Technologies).
Sequencing libraries were generated using the Kappa LTP library preparation kit (Kappa Biosystems) using the manufacturer's protocol. Briefly, the workflow included fragmentation of double stranded cDNA, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification steps.

treatment_protocol: Mice were infected via retro orbital injection with 2 x 10^6 PFU of LCMV-Cl13

tag: mouse strain

tag: tissue source

value: spleen

tag: cell phenotype

tag: infection

value: LCMV-Cl13 infected


title: TDRD6 KnockOut (Tdrd6-/-) 1

tag: strain background

tag: genotype/variation

tag: tissue


title: Immunosuppressive dendritic cells from LCMV-Cl13 infected mice


title: R-H3K27ac ChIP

source_name: R-H3K27ac ChIP

tag: cell type

tag: chip antibody vendor

value: Active Motif


title: R-H3K4me3 ChIP

source_name: R-H3K4me3 ChIP

tag: cell line of origin

value: Abcam


title: R-H3K4me1 ChIP

source_name: R-H3K4me1 ChIP

value: embryonic stem cells (ESCs; R cells)


title: R-IgG ChIP

source_name: R-IgG ChIP

value: Lif 2i

value: IgG (normal rabbit)

value: Invitrogen


title: Dendritic cells from uninfected mice

source_name: naïve (uninfected) mice


title: MNase-seq in H4K44->R mutant yeast grown in YPA, rep #2

status: Public on Dec 07 2015

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Demultiplexing was accomplished using bcl2fastq
Alignment: bowtie v0.12.7, command-line parameters -m 1 --best
Track generation: MNase-seq BED files were rendered as bedGraphs using the BEDtools genomeCoverageBed utility; these were then RPM-adjusted. Resulting bedGraphs were converted to tracks using UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: sacCer2
Supplementary_files_format_and_content: BigWigs are per-base pair track visualizations of the MNase-seq data after RPM adjustment.

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: See treatment protocol

extract_protocol:
MNase digestion assays were performed as described previously (Rando, O.J. (2010). Genome-wide mapping of nucleosomes in yeast. Methods in enzymology 470, 105-118.). Briefly, after collection, the cells were cross-linked with formaldehyde, the cell wall was digested with Zymolyase, and the chromatin was digested with a titration of MNase. The resulting DNA was electrophoresed on an agarose gel, and an ideal digestion in which most of the genome (>80%) was digested into a mono-nucleosome was chosen.
Mononucleosomal DNA was isolated and end-repaired for library preparation. MNase-seq libraries were constructed with NEBNext® Ultra™ DNA Library Prep Kit for Illumina®. The DNA was size selected and ampliﬁed by PCR using the adaptor primers. The ampliﬁed DNA was then puriﬁed and used for cluster generation and sequencing on the Illumina® HiSeq or NextSeq system.

treatment_protocol: SK1 diploid yeast were first grown in YPD (2% dextrose, 2% bacto-peptone, 1% bacto yeast extract) from a starting OD600 of 0.2 to final OD600 of 0.8, and then transferred in YPA (2% KAc, 2% bacto-peptone, 1% bacto yeast extract) from an OD600 of 0.02 to 0.5–0.8 at 30°C. Cells were washed once with water and then inoculated into sporulation media (2% KAc supplemented for auxotrophic amino acids) at 2.0 OD600 and incubated at 30°C with vigorous agitation. Sporulation efficiency was determined typically after 48 h of induction by counting asci visualized by light microscopy. Cells were extracted for chIP-seq at 4hrs post-sporulation.

tag: strain

tag: genetic background

value: Mutant

tag: growth media

value: YPA

tag: replicate


title: MNase-seq in WT yeast grown in YPA, rep #1

value: WT


title: MNase-seq in H4K44->R mutant yeast grown in YPD, rep #2

value: YPD


title: MNase-seq in WT yeast grown in YPD, rep #2


title: MNase-seq in H4K44->R mutant yeast grown in YPA, rep #1


title: MNase-seq in H4K44->R mutant yeast grown in YPD, rep #1


title: TDRD6 Heterozygote (Tdrd6+/-) 4

value: TDRD6 Heterozygote (Tdrd6+/-)

value: postnatal date 26 (P26)

value: testis

value: post meiotic cells

value: round spermatids


title: Input in WT yeast, rep #1

data_processing:
Demultiplexing was accomplished using bcl2fastq
Alignment: bowtie v0.12.7, command-line parameters -m 1 --best
Track generation: Rad51 and input BED files were rendered as bedGraphs using the BEDtools genomeCoverageBed utility; these were then RPM-adjusted individually and input was subtracted from Rad51. The final files have Rad51 (both replicates) minus input (single replicate) for WT and H4K44R mutant yeast. Resulting bedGraphs were converted to tracks using UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: sacCer2
Supplementary_files_format_and_content: BigWigs are per-base pair track visualizations of the Rad51 data, RPM-adjusted and input-subtracted

extract_protocol:
Sporulating cell samples at different time point were cross-linked with 1% formaldehyde at room temperature for 15 minutes immediately after harvesting. Chromatin immunoprecipitation (ChIP) assays were performed as described in (Govin, J., Schug, J., Krishnamoorthy, T., Dorsey, J., Khochbin, S., and Berger, S.L. (2010b). Genome-wide mapping of histone H4 serine-1 phosphorylation during sporulation in Saccharomyces cerevisiae. Nucleic acids research 38, 4599-4606.) and followed by library preparation.
ChIP-seq libraries were prepared using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® in accordance with the manufacturer’s instructions and subjected to single-end sequencing using an Illumina® NextSeq instrument.

tag: ChIP

value: Input

tag: antibody

value: Santa Cruz Biotechnology (sc-33626)


title: Rad51 chIP-seq in H4K44->R mutant yeast, rep #2


title: Monocytes from uninfected mice

value: bone marrow


title: Rad51 chIP-seq in WT yeast, rep #2


title: H3 chIP-seq in WT yeast, rep #1

data_processing:
Demultiplexing was accomplished using in-house scripts to handle dual-indexed data
Alignment: bowtie v0.12.7, command-line parameters -m 1 --best
Track generation: aligned tag BED files were trimmed to 50bp and rendered as bedGraphs using the BEDtools genomeCoverageBed utility; these were then RPKM-adjusted (divided by the number of billions of bases aligned) individually and H3 was subtracted from H3K4me3 and H3K56ac in a background-matched, replicate matched fashion. The final files have H3 PTMs (both replicates) minus H3 (for that replicate) for WT and H4K44R mutant yeast. Resulting bedGraphs were converted to tracks using UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: sacCer2
Supplementary_files_format_and_content: BigWigs are per-base pair track visualizations of the H3K4me3 and H3K56ac data, RPKM-adjusted and H3-subtracted

value: Abcam (ab1791)


title: H3 chIP-seq in WT yeast, rep #2


title: H3 chIP-seq in H4K44->R mutant yeast, rep #2


title: Rad51 chIP-seq in WT yeast, rep #1


title: Rad51 chIP-seq in H4K44->R mutant yeast, rep #1


title: H3K56ac chIP-seq in H4K44->R mutant yeast, rep #1

value: Active Motif (39281)


title: H3K56ac chIP-seq in H4K44->R mutant yeast, rep #2


title: H3K56ac chIP-seq in WT yeast, rep #2


title: H3K4me3 chIP-seq in H4K44->R mutant yeast, rep #2

value: Abcam (ab8580)


title: H3K4me3 chIP-seq in WT yeast, rep #2


title: H3K56ac chIP-seq in WT yeast, rep #1


title: MNase-seq in WT yeast grown in YPA, rep #2


title: H3K4me3 chIP-seq in WT yeast, rep #1


title: Input in H4K44->R mutant yeast, rep #1


title: MNase-seq in WT yeast grown in YPD, rep #1


title: fetal3_H8_fetal_13wpc

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

description:
Single cell H8 from experiment fetal neocortex at 13 wpc
fetal3_H8_fetal_13wpc

data_processing:
"freeIbis" was used as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.)
"leeHom" was used to trim adapters and merge Illumina sequencing reads. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.)
"deML" was used for robust demultiplexing of Illumina sequences using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.)
Reads were aligned against the human genome (build GRCh38.77 from ENSEMBLE) using TopHat v2.0.14. The genome was indexed using Bowtie v2.2.6
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks v2.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Master data frame including sample name, gene ID, and FPKM values for each single cell.

source_name: fetal human cortex 2

growth_protocol: Fetuses were 12 to 13 wpc as assessed by ultrasound measurements of crown-rump length and other standard criteria of developmental stage determination.

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Fetal cortices were digested with papain (Miltenyi Biotec, 1ml) for 15 min at 37°C on a rotating wheel, followed by addition of a papain inhibitor. Dissociated cells were filtered through 40, 30, and 20 μm diameter strainers to create a single cell suspension.

tag: Stage

value: 13 weeks post-conception

value: Fetal neocortex


title: fetal3_H5_fetal_13wpc

description:
Single cell H5 from experiment fetal neocortex at 13 wpc
fetal3_H5_fetal_13wpc


title: fetal3_H2_fetal_13wpc

description:
Single cell H2 from experiment fetal neocortex at 13 wpc
fetal3_H2_fetal_13wpc


title: fetal3_G8_fetal_13wpc

description:
Single cell G8 from experiment fetal neocortex at 13 wpc
fetal3_G8_fetal_13wpc


title: H3K4me3 chIP-seq in H4K44->R mutant yeast, rep #1

value: Mutant


title: fetal3_G7_fetal_13wpc

description:
Single cell G7 from experiment fetal neocortex at 13 wpc
fetal3_G7_fetal_13wpc


title: fetal3_H9_fetal_13wpc

description:
Single cell H9 from experiment fetal neocortex at 13 wpc
fetal3_H9_fetal_13wpc


title: fetal3_G9_fetal_13wpc

description:
Single cell G9 from experiment fetal neocortex at 13 wpc
fetal3_G9_fetal_13wpc


title: fetal3_H6_fetal_13wpc

description:
Single cell H6 from experiment fetal neocortex at 13 wpc
fetal3_H6_fetal_13wpc


title: fetal3_H7_fetal_13wpc

description:
Single cell H7 from experiment fetal neocortex at 13 wpc
fetal3_H7_fetal_13wpc


title: fetal3_H11_fetal_13wpc

description:
Single cell H11 from experiment fetal neocortex at 13 wpc
fetal3_H11_fetal_13wpc


title: fetal3_G5_fetal_13wpc

description:
Single cell G5 from experiment fetal neocortex at 13 wpc
fetal3_G5_fetal_13wpc


title: fetal3_H4_fetal_13wpc

description:
Single cell H4 from experiment fetal neocortex at 13 wpc
fetal3_H4_fetal_13wpc


title: fetal3_G6_fetal_13wpc

description:
Single cell G6 from experiment fetal neocortex at 13 wpc
fetal3_G6_fetal_13wpc


title: fetal3_G2_fetal_13wpc

description:
Single cell G2 from experiment fetal neocortex at 13 wpc
fetal3_G2_fetal_13wpc


title: fetal3_F1_fetal_13wpc

description:
Single cell F1 from experiment fetal neocortex at 13 wpc
fetal3_F1_fetal_13wpc


title: fetal3_F6_fetal_13wpc

description:
Single cell F6 from experiment fetal neocortex at 13 wpc
fetal3_F6_fetal_13wpc


title: fetal3_F7_fetal_13wpc

description:
Single cell F7 from experiment fetal neocortex at 13 wpc
fetal3_F7_fetal_13wpc


title: fetal3_F3_fetal_13wpc

description:
Single cell F3 from experiment fetal neocortex at 13 wpc
fetal3_F3_fetal_13wpc


title: fetal3_G1_fetal_13wpc

description:
Single cell G1 from experiment fetal neocortex at 13 wpc
fetal3_G1_fetal_13wpc


title: fetal3_G11_fetal_13wpc

description:
Single cell G11 from experiment fetal neocortex at 13 wpc
fetal3_G11_fetal_13wpc


title: fetal3_F11_fetal_13wpc

description:
Single cell F11 from experiment fetal neocortex at 13 wpc
fetal3_F11_fetal_13wpc


title: fetal3_G10_fetal_13wpc

description:
Single cell G10 from experiment fetal neocortex at 13 wpc
fetal3_G10_fetal_13wpc


title: fetal3_F8_fetal_13wpc

description:
Single cell F8 from experiment fetal neocortex at 13 wpc
fetal3_F8_fetal_13wpc


title: fetal3_F2_fetal_13wpc

description:
Single cell F2 from experiment fetal neocortex at 13 wpc
fetal3_F2_fetal_13wpc


title: fetal3_H1_fetal_13wpc

description:
Single cell H1 from experiment fetal neocortex at 13 wpc
fetal3_H1_fetal_13wpc


title: H3 chIP-seq in H4K44->R mutant yeast, rep #1


title: fetal3_E2_fetal_13wpc

description:
Single cell E2 from experiment fetal neocortex at 13 wpc
fetal3_E2_fetal_13wpc


title: fetal3_E4_fetal_13wpc

description:
Single cell E4 from experiment fetal neocortex at 13 wpc
fetal3_E4_fetal_13wpc


title: fetal3_F10_fetal_13wpc

description:
Single cell F10 from experiment fetal neocortex at 13 wpc
fetal3_F10_fetal_13wpc


title: fetal3_E5_fetal_13wpc

description:
Single cell E5 from experiment fetal neocortex at 13 wpc
fetal3_E5_fetal_13wpc


title: fetal3_E10_fetal_13wpc

description:
Single cell E10 from experiment fetal neocortex at 13 wpc
fetal3_E10_fetal_13wpc


title: fetal3_E11_fetal_13wpc

description:
Single cell E11 from experiment fetal neocortex at 13 wpc
fetal3_E11_fetal_13wpc


title: fetal3_F5_fetal_13wpc

description:
Single cell F5 from experiment fetal neocortex at 13 wpc
fetal3_F5_fetal_13wpc


title: fetal3_D8_fetal_13wpc

description:
Single cell D8 from experiment fetal neocortex at 13 wpc
fetal3_D8_fetal_13wpc


title: fetal3_D9_fetal_13wpc

description:
Single cell D9 from experiment fetal neocortex at 13 wpc
fetal3_D9_fetal_13wpc


title: fetal3_E3_fetal_13wpc

description:
Single cell E3 from experiment fetal neocortex at 13 wpc
fetal3_E3_fetal_13wpc


title: fetal3_D10_fetal_13wpc

description:
Single cell D10 from experiment fetal neocortex at 13 wpc
fetal3_D10_fetal_13wpc


title: fetal3_D4_fetal_13wpc

description:
Single cell D4 from experiment fetal neocortex at 13 wpc
fetal3_D4_fetal_13wpc


title: fetal3_C9_fetal_13wpc

description:
Single cell C9 from experiment fetal neocortex at 13 wpc
fetal3_C9_fetal_13wpc


title: fetal3_D3_fetal_13wpc

description:
Single cell D3 from experiment fetal neocortex at 13 wpc
fetal3_D3_fetal_13wpc


title: fetal3_D2_fetal_13wpc

description:
Single cell D2 from experiment fetal neocortex at 13 wpc
fetal3_D2_fetal_13wpc


title: fetal3_C5_fetal_13wpc

description:
Single cell C5 from experiment fetal neocortex at 13 wpc
fetal3_C5_fetal_13wpc


title: fetal3_C12_fetal_13wpc

description:
Single cell C12 from experiment fetal neocortex at 13 wpc
fetal3_C12_fetal_13wpc


title: fetal3_C4_fetal_13wpc

description:
Single cell C4 from experiment fetal neocortex at 13 wpc
fetal3_C4_fetal_13wpc


title: fetal3_C11_fetal_13wpc

description:
Single cell C11 from experiment fetal neocortex at 13 wpc
fetal3_C11_fetal_13wpc


title: fetal3_C10_fetal_13wpc

description:
Single cell C10 from experiment fetal neocortex at 13 wpc
fetal3_C10_fetal_13wpc


title: fetal3_B6_fetal_13wpc

description:
Single cell B6 from experiment fetal neocortex at 13 wpc
fetal3_B6_fetal_13wpc


title: fetal3_B8_fetal_13wpc

description:
Single cell B8 from experiment fetal neocortex at 13 wpc
fetal3_B8_fetal_13wpc


title: fetal3_B7_fetal_13wpc

description:
Single cell B7 from experiment fetal neocortex at 13 wpc
fetal3_B7_fetal_13wpc


title: fetal3_B5_fetal_13wpc

description:
Single cell B5 from experiment fetal neocortex at 13 wpc
fetal3_B5_fetal_13wpc


title: fetal3_B2_fetal_13wpc

description:
Single cell B2 from experiment fetal neocortex at 13 wpc
fetal3_B2_fetal_13wpc


title: fetal3_B12_fetal_13wpc

description:
Single cell B12 from experiment fetal neocortex at 13 wpc
fetal3_B12_fetal_13wpc


title: fetal3_B11_fetal_13wpc

description:
Single cell B11 from experiment fetal neocortex at 13 wpc
fetal3_B11_fetal_13wpc


title: fetal3_E1_fetal_13wpc

description:
Single cell E1 from experiment fetal neocortex at 13 wpc
fetal3_E1_fetal_13wpc


title: fetal3_B10_fetal_13wpc

description:
Single cell B10 from experiment fetal neocortex at 13 wpc
fetal3_B10_fetal_13wpc


title: fetal3_A6_fetal_13wpc

description:
Single cell A6 from experiment fetal neocortex at 13 wpc
fetal3_A6_fetal_13wpc


title: fetal3_A8_fetal_13wpc

description:
Single cell A8 from experiment fetal neocortex at 13 wpc
fetal3_A8_fetal_13wpc


title: fetal3_C7_fetal_13wpc

description:
Single cell C7 from experiment fetal neocortex at 13 wpc
fetal3_C7_fetal_13wpc


title: fetal2_H7_fetal_12wpc_c2

description:
Single cell H7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H7_fetal_12wpc_c2

source_name: fetal human cortex 1

value: 12 weeks post-conception


title: fetal3_A12_fetal_13wpc

description:
Single cell A12 from experiment fetal neocortex at 13 wpc
fetal3_A12_fetal_13wpc


title: fetal3_A9_fetal_13wpc

description:
Single cell A9 from experiment fetal neocortex at 13 wpc
fetal3_A9_fetal_13wpc


title: fetal2_H5_fetal_12wpc_c2

description:
Single cell H5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H5_fetal_12wpc_c2


title: fetal2_H8_fetal_12wpc_c2

description:
Single cell H8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H8_fetal_12wpc_c2


title: fetal2_H2_fetal_12wpc_c2

description:
Single cell H2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H2_fetal_12wpc_c2


title: fetal2_H6_fetal_12wpc_c2

description:
Single cell H6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H6_fetal_12wpc_c2


title: fetal2_H4_fetal_12wpc_c2

description:
Single cell H4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H4_fetal_12wpc_c2


title: fetal2_G9_fetal_12wpc_c2

description:
Single cell G9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G9_fetal_12wpc_c2


title: fetal3_A4_fetal_13wpc

description:
Single cell A4 from experiment fetal neocortex at 13 wpc
fetal3_A4_fetal_13wpc


title: fetal2_H1_fetal_12wpc_c2

description:
Single cell H1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H1_fetal_12wpc_c2


title: fetal2_G7_fetal_12wpc_c2

description:
Single cell G7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G7_fetal_12wpc_c2


title: fetal2_H11_fetal_12wpc_c2

description:
Single cell H11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H11_fetal_12wpc_c2


title: fetal3_B3_fetal_13wpc

description:
Single cell B3 from experiment fetal neocortex at 13 wpc
fetal3_B3_fetal_13wpc


title: fetal2_G2_fetal_12wpc_c2

description:
Single cell G2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G2_fetal_12wpc_c2


title: fetal2_G1_fetal_12wpc_c2

description:
Single cell G1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G1_fetal_12wpc_c2


title: fetal2_G12_fetal_12wpc_c2

description:
Single cell G12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G12_fetal_12wpc_c2


title: fetal2_G3_fetal_12wpc_c2

description:
Single cell G3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G3_fetal_12wpc_c2


title: fetal2_G4_fetal_12wpc_c2

description:
Single cell G4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G4_fetal_12wpc_c2


title: fetal2_F7_fetal_12wpc_c2

description:
Single cell F7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F7_fetal_12wpc_c2


title: fetal2_F6_fetal_12wpc_c2

description:
Single cell F6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F6_fetal_12wpc_c2


title: fetal2_F4_fetal_12wpc_c2

description:
Single cell F4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F4_fetal_12wpc_c2


title: fetal2_F5_fetal_12wpc_c2

description:
Single cell F5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F5_fetal_12wpc_c2


title: fetal2_F1_fetal_12wpc_c2

description:
Single cell F1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F1_fetal_12wpc_c2


title: fetal2_E9_fetal_12wpc_c2

description:
Single cell E9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E9_fetal_12wpc_c2


title: fetal2_F3_fetal_12wpc_c2

description:
Single cell F3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F3_fetal_12wpc_c2


title: fetal2_E2_fetal_12wpc_c2

description:
Single cell E2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E2_fetal_12wpc_c2


title: fetal2_E5_fetal_12wpc_c2

description:
Single cell E5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E5_fetal_12wpc_c2


title: fetal2_F2_fetal_12wpc_c2

description:
Single cell F2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F2_fetal_12wpc_c2


title: fetal2_E3_fetal_12wpc_c2

description:
Single cell E3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E3_fetal_12wpc_c2


title: fetal3_A7_fetal_13wpc

description:
Single cell A7 from experiment fetal neocortex at 13 wpc
fetal3_A7_fetal_13wpc


title: fetal2_E12_fetal_12wpc_c2

description:
Single cell E12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E12_fetal_12wpc_c2


title: fetal2_F12_fetal_12wpc_c2

description:
Single cell F12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F12_fetal_12wpc_c2


title: fetal2_E11_fetal_12wpc_c2

description:
Single cell E11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E11_fetal_12wpc_c2


title: fetal2_E1_fetal_12wpc_c2

description:
Single cell E1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E1_fetal_12wpc_c2


title: fetal2_D9_fetal_12wpc_c2

description:
Single cell D9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D9_fetal_12wpc_c2


title: fetal2_E8_fetal_12wpc_c2

description:
Single cell E8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E8_fetal_12wpc_c2


title: fetal2_D7_fetal_12wpc_c2

description:
Single cell D7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D7_fetal_12wpc_c2


title: fetal2_D4_fetal_12wpc_c2

description:
Single cell D4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D4_fetal_12wpc_c2


title: fetal2_D8_fetal_12wpc_c2

description:
Single cell D8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D8_fetal_12wpc_c2


title: fetal2_D2_fetal_12wpc_c2

description:
Single cell D2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D2_fetal_12wpc_c2


title: fetal2_D1_fetal_12wpc_c2

description:
Single cell D1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D1_fetal_12wpc_c2


title: fetal2_D10_fetal_12wpc_c2

description:
Single cell D10 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D10_fetal_12wpc_c2


title: fetal2_C8_fetal_12wpc_c2

description:
Single cell C8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C8_fetal_12wpc_c2


title: fetal2_C5_fetal_12wpc_c2

description:
Single cell C5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C5_fetal_12wpc_c2


title: fetal2_D11_fetal_12wpc_c2

description:
Single cell D11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D11_fetal_12wpc_c2


title: fetal2_D6_fetal_12wpc_c2

description:
Single cell D6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D6_fetal_12wpc_c2


title: fetal2_C4_fetal_12wpc_c2

description:
Single cell C4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C4_fetal_12wpc_c2


title: fetal2_C11_fetal_12wpc_c2

description:
Single cell C11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C11_fetal_12wpc_c2


title: fetal2_D3_fetal_12wpc_c2

description:
Single cell D3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D3_fetal_12wpc_c2


title: fetal2_E7_fetal_12wpc_c2

description:
Single cell E7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E7_fetal_12wpc_c2


title: fetal2_E4_fetal_12wpc_c2

description:
Single cell E4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E4_fetal_12wpc_c2


title: fetal2_B8_fetal_12wpc_c2

description:
Single cell B8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B8_fetal_12wpc_c2


title: fetal2_D12_fetal_12wpc_c2

description:
Single cell D12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D12_fetal_12wpc_c2


title: fetal2_B3_fetal_12wpc_c2

description:
Single cell B3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B3_fetal_12wpc_c2


title: fetal2_C9_fetal_12wpc_c2

description:
Single cell C9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C9_fetal_12wpc_c2


title: fetal2_C3_fetal_12wpc_c2

description:
Single cell C3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C3_fetal_12wpc_c2


title: fetal2_B7_fetal_12wpc_c2

description:
Single cell B7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B7_fetal_12wpc_c2


title: fetal2_A9_fetal_12wpc_c2

description:
Single cell A9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A9_fetal_12wpc_c2


title: fetal2_G6_fetal_12wpc_c2

description:
Single cell G6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G6_fetal_12wpc_c2


title: fetal2_A8_fetal_12wpc_c2

description:
Single cell A8 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A8_fetal_12wpc_c2


title: fetal2_D5_fetal_12wpc_c2

description:
Single cell D5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_D5_fetal_12wpc_c2


title: fetal2_C1_fetal_12wpc_c2

description:
Single cell C1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C1_fetal_12wpc_c2


title: fetal2_B11_fetal_12wpc_c2

description:
Single cell B11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B11_fetal_12wpc_c2


title: fetal2_B6_fetal_12wpc_c2

description:
Single cell B6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B6_fetal_12wpc_c2


title: fetal2_B1_fetal_12wpc_c2

description:
Single cell B1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B1_fetal_12wpc_c2


title: fetal2_B2_fetal_12wpc_c2

description:
Single cell B2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B2_fetal_12wpc_c2


title: fetal2_C2_fetal_12wpc_c2

description:
Single cell C2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C2_fetal_12wpc_c2


title: fetal2_B5_fetal_12wpc_c2

description:
Single cell B5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B5_fetal_12wpc_c2


title: fetal2_A12_fetal_12wpc_c2

description:
Single cell A12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A12_fetal_12wpc_c2


title: fetal2_A10_fetal_12wpc_c2

description:
Single cell A10 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A10_fetal_12wpc_c2


title: fetal2_B9_fetal_12wpc_c2

description:
Single cell B9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B9_fetal_12wpc_c2


title: fetal2_G11_fetal_12wpc_c2

description:
Single cell G11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G11_fetal_12wpc_c2


title: fetal2_B10_fetal_12wpc_c2

description:
Single cell B10 from experiment fetal neocortex at 12 wpc chip 2
fetal2_B10_fetal_12wpc_c2


title: fetal2_A7_fetal_12wpc_c2

description:
Single cell A7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A7_fetal_12wpc_c2


title: fetal2_E6_fetal_12wpc_c2

description:
Single cell E6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_E6_fetal_12wpc_c2


title: fetal2_A4_fetal_12wpc_c2

description:
Single cell A4 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A4_fetal_12wpc_c2


title: fetal2_A11_fetal_12wpc_c2

description:
Single cell A11 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A11_fetal_12wpc_c2


title: fetal2_A3_fetal_12wpc_c2

description:
Single cell A3 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A3_fetal_12wpc_c2


title: fetal2_A6_fetal_12wpc_c2

description:
Single cell A6 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A6_fetal_12wpc_c2


title: fetal1_G9_fetal_12wpc_c1

description:
Single cell G9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G9_fetal_12wpc_c1


title: fetal1_G7_fetal_12wpc_c1

description:
Single cell G7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G7_fetal_12wpc_c1


title: fetal2_A5_fetal_12wpc_c2

description:
Single cell A5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A5_fetal_12wpc_c2


title: fetal2_A2_fetal_12wpc_c2

description:
Single cell A2 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A2_fetal_12wpc_c2


title: fetal2_F9_fetal_12wpc_c2

description:
Single cell F9 from experiment fetal neocortex at 12 wpc chip 2
fetal2_F9_fetal_12wpc_c2


title: fetal1_H7_fetal_12wpc_c1

description:
Single cell H7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H7_fetal_12wpc_c1


title: fetal1_H12_fetal_12wpc_c1

description:
Single cell H12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H12_fetal_12wpc_c1


title: fetal2_A1_fetal_12wpc_c2

description:
Single cell A1 from experiment fetal neocortex at 12 wpc chip 2
fetal2_A1_fetal_12wpc_c2


title: fetal1_H6_fetal_12wpc_c1

description:
Single cell H6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H6_fetal_12wpc_c1


title: fetal1_G3_fetal_12wpc_c1

description:
Single cell G3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G3_fetal_12wpc_c1


title: fetal1_H2_fetal_12wpc_c1

description:
Single cell H2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H2_fetal_12wpc_c1


title: fetal1_H5_fetal_12wpc_c1

description:
Single cell H5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H5_fetal_12wpc_c1


title: fetal1_G2_fetal_12wpc_c1

description:
Single cell G2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G2_fetal_12wpc_c1


title: fetal1_H3_fetal_12wpc_c1

description:
Single cell H3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H3_fetal_12wpc_c1


title: fetal1_H11_fetal_12wpc_c1

description:
Single cell H11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H11_fetal_12wpc_c1


title: fetal1_G8_fetal_12wpc_c1

description:
Single cell G8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G8_fetal_12wpc_c1


title: fetal1_H10_fetal_12wpc_c1

description:
Single cell H10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H10_fetal_12wpc_c1


title: fetal2_G5_fetal_12wpc_c2

description:
Single cell G5 from experiment fetal neocortex at 12 wpc chip 2
fetal2_G5_fetal_12wpc_c2


title: fetal1_G1_fetal_12wpc_c1

description:
Single cell G1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G1_fetal_12wpc_c1


title: fetal1_G6_fetal_12wpc_c1

description:
Single cell G6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G6_fetal_12wpc_c1


title: fetal1_G5_fetal_12wpc_c1

description:
Single cell G5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G5_fetal_12wpc_c1


title: fetal1_H8_fetal_12wpc_c1

description:
Single cell H8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_H8_fetal_12wpc_c1


title: fetal1_G12_fetal_12wpc_c1

description:
Single cell G12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G12_fetal_12wpc_c1


title: fetal1_G4_fetal_12wpc_c1

description:
Single cell G4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G4_fetal_12wpc_c1


title: fetal1_F2_fetal_12wpc_c1

description:
Single cell F2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F2_fetal_12wpc_c1


title: fetal1_F3_fetal_12wpc_c1

description:
Single cell F3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F3_fetal_12wpc_c1


title: fetal1_G10_fetal_12wpc_c1

description:
Single cell G10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G10_fetal_12wpc_c1


title: fetal1_F4_fetal_12wpc_c1

description:
Single cell F4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F4_fetal_12wpc_c1


title: fetal1_F8_fetal_12wpc_c1

description:
Single cell F8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F8_fetal_12wpc_c1


title: fetal1_F11_fetal_12wpc_c1

description:
Single cell F11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F11_fetal_12wpc_c1


title: fetal1_F7_fetal_12wpc_c1

description:
Single cell F7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F7_fetal_12wpc_c1


title: fetal2_C7_fetal_12wpc_c2

description:
Single cell C7 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C7_fetal_12wpc_c2


title: fetal1_G11_fetal_12wpc_c1

description:
Single cell G11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_G11_fetal_12wpc_c1


title: fetal1_F1_fetal_12wpc_c1

description:
Single cell F1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F1_fetal_12wpc_c1


title: fetal1_F12_fetal_12wpc_c1

description:
Single cell F12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F12_fetal_12wpc_c1


title: fetal2_H12_fetal_12wpc_c2

description:
Single cell H12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_H12_fetal_12wpc_c2


title: fetal1_F10_fetal_12wpc_c1

description:
Single cell F10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F10_fetal_12wpc_c1


title: fetal1_E8_fetal_12wpc_c1

description:
Single cell E8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E8_fetal_12wpc_c1


title: fetal1_E5_fetal_12wpc_c1

description:
Single cell E5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E5_fetal_12wpc_c1


title: fetal1_E9_fetal_12wpc_c1

description:
Single cell E9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E9_fetal_12wpc_c1


title: fetal1_E7_fetal_12wpc_c1

description:
Single cell E7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E7_fetal_12wpc_c1


title: fetal1_E3_fetal_12wpc_c1

description:
Single cell E3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E3_fetal_12wpc_c1


title: fetal2_C12_fetal_12wpc_c2

description:
Single cell C12 from experiment fetal neocortex at 12 wpc chip 2
fetal2_C12_fetal_12wpc_c2


title: fetal1_E12_fetal_12wpc_c1

description:
Single cell E12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E12_fetal_12wpc_c1


title: fetal1_E1_fetal_12wpc_c1

description:
Single cell E1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E1_fetal_12wpc_c1


title: fetal1_F9_fetal_12wpc_c1

description:
Single cell F9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_F9_fetal_12wpc_c1


title: fetal1_E10_fetal_12wpc_c1

description:
Single cell E10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E10_fetal_12wpc_c1


title: fetal1_D9_fetal_12wpc_c1

description:
Single cell D9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D9_fetal_12wpc_c1


title: fetal1_D7_fetal_12wpc_c1

description:
Single cell D7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D7_fetal_12wpc_c1


title: fetal1_D8_fetal_12wpc_c1

description:
Single cell D8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D8_fetal_12wpc_c1


title: fetal1_D5_fetal_12wpc_c1

description:
Single cell D5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D5_fetal_12wpc_c1


title: fetal1_D6_fetal_12wpc_c1

description:
Single cell D6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D6_fetal_12wpc_c1


title: fetal1_D4_fetal_12wpc_c1

description:
Single cell D4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D4_fetal_12wpc_c1


title: fetal1_D2_fetal_12wpc_c1

description:
Single cell D2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D2_fetal_12wpc_c1


title: fetal1_D1_fetal_12wpc_c1

description:
Single cell D1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D1_fetal_12wpc_c1


title: fetal1_D10_fetal_12wpc_c1

description:
Single cell D10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D10_fetal_12wpc_c1


title: fetal1_D12_fetal_12wpc_c1

description:
Single cell D12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D12_fetal_12wpc_c1


title: fetal1_D11_fetal_12wpc_c1

description:
Single cell D11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_D11_fetal_12wpc_c1


title: fetal1_C6_fetal_12wpc_c1

description:
Single cell C6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C6_fetal_12wpc_c1


title: fetal1_E6_fetal_12wpc_c1

description:
Single cell E6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_E6_fetal_12wpc_c1


title: fetal1_C9_fetal_12wpc_c1

description:
Single cell C9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C9_fetal_12wpc_c1


title: fetal1_C2_fetal_12wpc_c1

description:
Single cell C2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C2_fetal_12wpc_c1


title: fetal1_C1_fetal_12wpc_c1

description:
Single cell C1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C1_fetal_12wpc_c1


title: fetal1_C10_fetal_12wpc_c1

description:
Single cell C10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C10_fetal_12wpc_c1


title: fetal1_B4_fetal_12wpc_c1

description:
Single cell B4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B4_fetal_12wpc_c1


title: fetal1_C12_fetal_12wpc_c1

description:
Single cell C12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C12_fetal_12wpc_c1


title: fetal1_B7_fetal_12wpc_c1

description:
Single cell B7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B7_fetal_12wpc_c1


title: fetal1_B6_fetal_12wpc_c1

description:
Single cell B6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B6_fetal_12wpc_c1


title: fetal1_C3_fetal_12wpc_c1

description:
Single cell C3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C3_fetal_12wpc_c1


title: fetal1_B3_fetal_12wpc_c1

description:
Single cell B3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B3_fetal_12wpc_c1


title: fetal1_B11_fetal_12wpc_c1

description:
Single cell B11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B11_fetal_12wpc_c1


title: fetal1_B12_fetal_12wpc_c1

description:
Single cell B12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B12_fetal_12wpc_c1


title: fetal1_B2_fetal_12wpc_c1

description:
Single cell B2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B2_fetal_12wpc_c1


title: fetal1_B10_fetal_12wpc_c1

description:
Single cell B10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B10_fetal_12wpc_c1


title: fetal1_B1_fetal_12wpc_c1

description:
Single cell B1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B1_fetal_12wpc_c1


title: fetal1_A8_fetal_12wpc_c1

description:
Single cell A8 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A8_fetal_12wpc_c1


title: fetal1_A5_fetal_12wpc_c1

description:
Single cell A5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A5_fetal_12wpc_c1


title: fetal1_A6_fetal_12wpc_c1

description:
Single cell A6 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A6_fetal_12wpc_c1


title: fetal1_A7_fetal_12wpc_c1

description:
Single cell A7 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A7_fetal_12wpc_c1


title: fetal1_A4_fetal_12wpc_c1

description:
Single cell A4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A4_fetal_12wpc_c1


title: fetal1_A2_fetal_12wpc_c1

description:
Single cell A2 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A2_fetal_12wpc_c1


title: fetal1_A1_fetal_12wpc_c1

description:
Single cell A1 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A1_fetal_12wpc_c1


title: fetal1_A3_fetal_12wpc_c1

description:
Single cell A3 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A3_fetal_12wpc_c1


title: fetal1_C4_fetal_12wpc_c1

description:
Single cell C4 from experiment fetal neocortex at 12 wpc chip 1
fetal1_C4_fetal_12wpc_c1


title: fetal1_A11_fetal_12wpc_c1

description:
Single cell A11 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A11_fetal_12wpc_c1


title: fetal1_B5_fetal_12wpc_c1

description:
Single cell B5 from experiment fetal neocortex at 12 wpc chip 1
fetal1_B5_fetal_12wpc_c1


title: mdOrg4_H3_hOrg_iPSC_reg4_58d

description:
Single cell H3 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_H3_hOrg_iPSC_reg4_58d

source_name: iPSC 409B2

growth_protocol: Cerebral organoids were generated using the same protocol as described Lancaster et al. Nature Protocols 2014, with the exception that mTESR1 (Stem Cell Technologies) was used during embryoid body formation.

treatment_protocol: Whole cerebral organoids and microdisseccted ventricles were dissociated in 2 ml of Accutase (StemPro) containing 0.2 U/µl Dnase I (Roche) for approximately 45 minutes. Dissociated cells were filtered through 40, 30, and 20 μm diameter strainers to create a single cell suspension.

value: 58 days

value: Microdissected cortical-like ventricle from cerebral organoid


title: mdOrg4_G9_hOrg_iPSC_reg4_58d

description:
Single cell G9 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G9_hOrg_iPSC_reg4_58d


title: mdOrg4_G8_hOrg_iPSC_reg4_58d

description:
Single cell G8 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G8_hOrg_iPSC_reg4_58d


title: mdOrg4_H9_hOrg_iPSC_reg4_58d

description:
Single cell H9 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_H9_hOrg_iPSC_reg4_58d


title: mdOrg4_G4_hOrg_iPSC_reg4_58d

description:
Single cell G4 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G4_hOrg_iPSC_reg4_58d


title: mdOrg4_G12_hOrg_iPSC_reg4_58d

description:
Single cell G12 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G12_hOrg_iPSC_reg4_58d


title: fetal1_A9_fetal_12wpc_c1

description:
Single cell A9 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A9_fetal_12wpc_c1


title: mdOrg4_F5_hOrg_iPSC_reg4_58d

description:
Single cell F5 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_F5_hOrg_iPSC_reg4_58d


title: mdOrg4_F8_hOrg_iPSC_reg4_58d

description:
Single cell F8 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_F8_hOrg_iPSC_reg4_58d


title: mdOrg4_G7_hOrg_iPSC_reg4_58d

description:
Single cell G7 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G7_hOrg_iPSC_reg4_58d


title: mdOrg4_G10_hOrg_iPSC_reg4_58d

description:
Single cell G10 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_G10_hOrg_iPSC_reg4_58d


title: mdOrg4_F10_hOrg_iPSC_reg4_58d

description:
Single cell F10 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_F10_hOrg_iPSC_reg4_58d


title: mdOrg4_H11_hOrg_iPSC_reg4_58d

description:
Single cell H11 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_H11_hOrg_iPSC_reg4_58d


title: mdOrg4_E5_hOrg_iPSC_reg4_58d

description:
Single cell E5 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E5_hOrg_iPSC_reg4_58d


title: mdOrg4_F12_hOrg_iPSC_reg4_58d

description:
Single cell F12 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_F12_hOrg_iPSC_reg4_58d


title: mdOrg4_E9_hOrg_iPSC_reg4_58d

description:
Single cell E9 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E9_hOrg_iPSC_reg4_58d


title: mdOrg4_E2_hOrg_iPSC_reg4_58d

description:
Single cell E2 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E2_hOrg_iPSC_reg4_58d


title: fetal1_A12_fetal_12wpc_c1

description:
Single cell A12 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A12_fetal_12wpc_c1


title: fetal1_A10_fetal_12wpc_c1

description:
Single cell A10 from experiment fetal neocortex at 12 wpc chip 1
fetal1_A10_fetal_12wpc_c1


title: mdOrg4_C8_hOrg_iPSC_reg4_58d

description:
Single cell C8 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_C8_hOrg_iPSC_reg4_58d


title: mdOrg4_D7_hOrg_iPSC_reg4_58d

description:
Single cell D7 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_D7_hOrg_iPSC_reg4_58d


title: mdOrg4_E10_hOrg_iPSC_reg4_58d

description:
Single cell E10 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E10_hOrg_iPSC_reg4_58d


title: mdOrg4_C4_hOrg_iPSC_reg4_58d

description:
Single cell C4 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_C4_hOrg_iPSC_reg4_58d


title: mdOrg4_D4_hOrg_iPSC_reg4_58d

description:
Single cell D4 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_D4_hOrg_iPSC_reg4_58d


title: mdOrg4_D12_hOrg_iPSC_reg4_58d

description:
Single cell D12 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_D12_hOrg_iPSC_reg4_58d


title: mdOrg4_C7_hOrg_iPSC_reg4_58d

description:
Single cell C7 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_C7_hOrg_iPSC_reg4_58d


title: mdOrg4_C12_hOrg_iPSC_reg4_58d

description:
Single cell C12 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_C12_hOrg_iPSC_reg4_58d


title: mdOrg4_B4_hOrg_iPSC_reg4_58d

description:
Single cell B4 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_B4_hOrg_iPSC_reg4_58d


title: mdOrg4_B2_hOrg_iPSC_reg4_58d

description:
Single cell B2 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_B2_hOrg_iPSC_reg4_58d


title: mdOrg4_B10_hOrg_iPSC_reg4_58d

description:
Single cell B10 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_B10_hOrg_iPSC_reg4_58d


title: mdOrg4_A6_hOrg_iPSC_reg4_58d

description:
Single cell A6 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_A6_hOrg_iPSC_reg4_58d


title: mdOrg4_B12_hOrg_iPSC_reg4_58d

description:
Single cell B12 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_B12_hOrg_iPSC_reg4_58d


title: mdOrg4_E3_hOrg_iPSC_reg4_58d

description:
Single cell E3 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E3_hOrg_iPSC_reg4_58d


title: mdOrg4_A4_hOrg_iPSC_reg4_58d

description:
Single cell A4 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_A4_hOrg_iPSC_reg4_58d


title: mdOrg4_A1_hOrg_iPSC_reg4_58d

description:
Single cell A1 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_A1_hOrg_iPSC_reg4_58d


title: mdOrg3_H9_hOrg_iPSC_reg3_58d

description:
Single cell H9 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_H9_hOrg_iPSC_reg3_58d


title: mdOrg4_E6_hOrg_iPSC_reg4_58d

description:
Single cell E6 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_E6_hOrg_iPSC_reg4_58d


title: mdOrg4_A11_hOrg_iPSC_reg4_58d

description:
Single cell A11 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_A11_hOrg_iPSC_reg4_58d


title: mdOrg3_H11_hOrg_iPSC_reg3_58d

description:
Single cell H11 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_H11_hOrg_iPSC_reg3_58d


title: mdOrg3_H10_hOrg_iPSC_reg3_58d

description:
Single cell H10 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_H10_hOrg_iPSC_reg3_58d


title: mdOrg3_G3_hOrg_iPSC_reg3_58d

description:
Single cell G3 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_G3_hOrg_iPSC_reg3_58d


title: mdOrg3_G4_hOrg_iPSC_reg3_58d

description:
Single cell G4 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_G4_hOrg_iPSC_reg3_58d


title: mdOrg3_H12_hOrg_iPSC_reg3_58d

description:
Single cell H12 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_H12_hOrg_iPSC_reg3_58d


title: mdOrg3_G12_hOrg_iPSC_reg3_58d

description:
Single cell G12 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_G12_hOrg_iPSC_reg3_58d


title: mdOrg3_F7_hOrg_iPSC_reg3_58d

description:
Single cell F7 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_F7_hOrg_iPSC_reg3_58d


title: mdOrg3_F1_hOrg_iPSC_reg3_58d

description:
Single cell F1 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_F1_hOrg_iPSC_reg3_58d


title: mdOrg3_E9_hOrg_iPSC_reg3_58d

description:
Single cell E9 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E9_hOrg_iPSC_reg3_58d


title: mdOrg3_F3_hOrg_iPSC_reg3_58d

description:
Single cell F3 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_F3_hOrg_iPSC_reg3_58d


title: mdOrg3_E8_hOrg_iPSC_reg3_58d

description:
Single cell E8 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E8_hOrg_iPSC_reg3_58d


title: mdOrg3_E5_hOrg_iPSC_reg3_58d

description:
Single cell E5 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E5_hOrg_iPSC_reg3_58d


title: mdOrg3_E4_hOrg_iPSC_reg3_58d

description:
Single cell E4 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E4_hOrg_iPSC_reg3_58d


title: mdOrg4_B8_hOrg_iPSC_reg4_58d

description:
Single cell B8 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_B8_hOrg_iPSC_reg4_58d


title: mdOrg3_G9_hOrg_iPSC_reg3_58d

description:
Single cell G9 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_G9_hOrg_iPSC_reg3_58d


title: mdOrg3_E3_hOrg_iPSC_reg3_58d

description:
Single cell E3 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E3_hOrg_iPSC_reg3_58d


title: mdOrg3_D9_hOrg_iPSC_reg3_58d

description:
Single cell D9 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_D9_hOrg_iPSC_reg3_58d


title: mdOrg3_D10_hOrg_iPSC_reg3_58d

description:
Single cell D10 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_D10_hOrg_iPSC_reg3_58d


title: mdOrg3_E2_hOrg_iPSC_reg3_58d

description:
Single cell E2 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E2_hOrg_iPSC_reg3_58d


title: mdOrg3_C8_hOrg_iPSC_reg3_58d

description:
Single cell C8 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C8_hOrg_iPSC_reg3_58d


title: mdOrg3_C4_hOrg_iPSC_reg3_58d

description:
Single cell C4 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C4_hOrg_iPSC_reg3_58d


title: mdOrg3_E7_hOrg_iPSC_reg3_58d

description:
Single cell E7 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_E7_hOrg_iPSC_reg3_58d


title: mdOrg3_D8_hOrg_iPSC_reg3_58d

description:
Single cell D8 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_D8_hOrg_iPSC_reg3_58d


title: mdOrg3_C11_hOrg_iPSC_reg3_58d

description:
Single cell C11 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C11_hOrg_iPSC_reg3_58d


title: mdOrg3_C7_hOrg_iPSC_reg3_58d

description:
Single cell C7 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C7_hOrg_iPSC_reg3_58d


title: mdOrg3_C1_hOrg_iPSC_reg3_58d

description:
Single cell C1 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C1_hOrg_iPSC_reg3_58d


title: mdOrg3_C5_hOrg_iPSC_reg3_58d

description:
Single cell C5 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C5_hOrg_iPSC_reg3_58d


title: mdOrg3_B3_hOrg_iPSC_reg3_58d

description:
Single cell B3 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B3_hOrg_iPSC_reg3_58d


title: mdOrg3_B8_hOrg_iPSC_reg3_58d

description:
Single cell B8 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B8_hOrg_iPSC_reg3_58d


title: mdOrg3_B9_hOrg_iPSC_reg3_58d

description:
Single cell B9 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B9_hOrg_iPSC_reg3_58d


title: mdOrg3_B10_hOrg_iPSC_reg3_58d

description:
Single cell B10 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B10_hOrg_iPSC_reg3_58d


title: mdOrg3_B5_hOrg_iPSC_reg3_58d

description:
Single cell B5 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B5_hOrg_iPSC_reg3_58d


title: mdOrg3_B2_hOrg_iPSC_reg3_58d

description:
Single cell B2 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B2_hOrg_iPSC_reg3_58d


title: mdOrg3_A5_hOrg_iPSC_reg3_58d

description:
Single cell A5 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_A5_hOrg_iPSC_reg3_58d


title: mdOrg3_C6_hOrg_iPSC_reg3_58d

description:
Single cell C6 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_C6_hOrg_iPSC_reg3_58d


title: mdOrg2_H8_hOrg_ESC_reg2_53d

description:
Single cell H8 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H8_hOrg_ESC_reg2_53d

source_name: ESC H9

value: 53 days


title: mdOrg3_B12_hOrg_iPSC_reg3_58d

description:
Single cell B12 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B12_hOrg_iPSC_reg3_58d


title: mdOrg2_H4_hOrg_ESC_reg2_53d

description:
Single cell H4 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H4_hOrg_ESC_reg2_53d


title: mdOrg3_D11_hOrg_iPSC_reg3_58d

description:
Single cell D11 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_D11_hOrg_iPSC_reg3_58d


title: mdOrg2_H12_hOrg_ESC_reg2_53d

description:
Single cell H12 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H12_hOrg_ESC_reg2_53d


title: mdOrg4_C11_hOrg_iPSC_reg4_58d

description:
Single cell C11 from human cerebral organoid experiment micro-dissected region 4 58d
mdOrg4_C11_hOrg_iPSC_reg4_58d


title: mdOrg2_H2_hOrg_ESC_reg2_53d

description:
Single cell H2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H2_hOrg_ESC_reg2_53d


title: mdOrg3_B11_hOrg_iPSC_reg3_58d

description:
Single cell B11 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B11_hOrg_iPSC_reg3_58d


title: mdOrg2_H10_hOrg_ESC_reg2_53d

description:
Single cell H10 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H10_hOrg_ESC_reg2_53d


title: mdOrg3_A8_hOrg_iPSC_reg3_58d

description:
Single cell A8 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_A8_hOrg_iPSC_reg3_58d


title: mdOrg3_A10_hOrg_iPSC_reg3_58d

description:
Single cell A10 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_A10_hOrg_iPSC_reg3_58d


title: mdOrg3_B1_hOrg_iPSC_reg3_58d

description:
Single cell B1 from human cerebral organoid experiment micro-dissected region 3 58d
mdOrg3_B1_hOrg_iPSC_reg3_58d


title: mdOrg2_H6_hOrg_ESC_reg2_53d

description:
Single cell H6 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H6_hOrg_ESC_reg2_53d


title: mdOrg2_G9_hOrg_ESC_reg2_53d

description:
Single cell G9 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G9_hOrg_ESC_reg2_53d


title: mdOrg2_G3_hOrg_ESC_reg2_53d

description:
Single cell G3 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G3_hOrg_ESC_reg2_53d


title: mdOrg2_H11_hOrg_ESC_reg2_53d

description:
Single cell H11 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H11_hOrg_ESC_reg2_53d


title: mdOrg2_G2_hOrg_ESC_reg2_53d

description:
Single cell G2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G2_hOrg_ESC_reg2_53d


title: mdOrg2_G10_hOrg_ESC_reg2_53d

description:
Single cell G10 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G10_hOrg_ESC_reg2_53d


title: mdOrg2_F7_hOrg_ESC_reg2_53d

description:
Single cell F7 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F7_hOrg_ESC_reg2_53d


title: mdOrg2_G1_hOrg_ESC_reg2_53d

description:
Single cell G1 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G1_hOrg_ESC_reg2_53d


title: mdOrg2_F3_hOrg_ESC_reg2_53d

description:
Single cell F3 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F3_hOrg_ESC_reg2_53d


title: mdOrg2_F6_hOrg_ESC_reg2_53d

description:
Single cell F6 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F6_hOrg_ESC_reg2_53d


title: mdOrg2_E9_hOrg_ESC_reg2_53d

description:
Single cell E9 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_E9_hOrg_ESC_reg2_53d


title: mdOrg2_F2_hOrg_ESC_reg2_53d

description:
Single cell F2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F2_hOrg_ESC_reg2_53d


title: mdOrg2_F5_hOrg_ESC_reg2_53d

description:
Single cell F5 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F5_hOrg_ESC_reg2_53d


title: mdOrg2_E8_hOrg_ESC_reg2_53d

description:
Single cell E8 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_E8_hOrg_ESC_reg2_53d


title: mdOrg2_E6_hOrg_ESC_reg2_53d

description:
Single cell E6 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_E6_hOrg_ESC_reg2_53d


title: mdOrg2_D8_hOrg_ESC_reg2_53d

description:
Single cell D8 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D8_hOrg_ESC_reg2_53d


title: mdOrg2_H5_hOrg_ESC_reg2_53d

description:
Single cell H5 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_H5_hOrg_ESC_reg2_53d


title: mdOrg2_G8_hOrg_ESC_reg2_53d

description:
Single cell G8 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_G8_hOrg_ESC_reg2_53d


title: mdOrg2_F12_hOrg_ESC_reg2_53d

description:
Single cell F12 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_F12_hOrg_ESC_reg2_53d


title: mdOrg2_D6_hOrg_ESC_reg2_53d

description:
Single cell D6 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D6_hOrg_ESC_reg2_53d


title: mdOrg2_E2_hOrg_ESC_reg2_53d

description:
Single cell E2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_E2_hOrg_ESC_reg2_53d


title: mdOrg2_D7_hOrg_ESC_reg2_53d

description:
Single cell D7 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D7_hOrg_ESC_reg2_53d


title: mdOrg2_D12_hOrg_ESC_reg2_53d

description:
Single cell D12 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D12_hOrg_ESC_reg2_53d


title: mdOrg2_D11_hOrg_ESC_reg2_53d

description:
Single cell D11 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D11_hOrg_ESC_reg2_53d


title: mdOrg2_D5_hOrg_ESC_reg2_53d

description:
Single cell D5 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D5_hOrg_ESC_reg2_53d


title: mdOrg2_D4_hOrg_ESC_reg2_53d

description:
Single cell D4 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D4_hOrg_ESC_reg2_53d


title: mdOrg2_D2_hOrg_ESC_reg2_53d

description:
Single cell D2 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D2_hOrg_ESC_reg2_53d


title: mdOrg2_D10_hOrg_ESC_reg2_53d

description:
Single cell D10 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_D10_hOrg_ESC_reg2_53d


title: mdOrg2_B6_hOrg_ESC_reg2_53d

description:
Single cell B6 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_B6_hOrg_ESC_reg2_53d


title: mdOrg2_C3_hOrg_ESC_reg2_53d

description:
Single cell C3 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_C3_hOrg_ESC_reg2_53d


title: mdOrg2_C11_hOrg_ESC_reg2_53d

description:
Single cell C11 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_C11_hOrg_ESC_reg2_53d


title: mdOrg2_C4_hOrg_ESC_reg2_53d

description:
Single cell C4 from human cerebral organoid experiment micro-dissected region 2 53d
mdOrg2_C4_hOrg_ESC_reg2_53d