title: Cup.rep2.Neg.Plate2.E11


title: Cup.rep2.Neg.Plate1.G11

status: Public on Jun 11 2024

type: SRA

city: St. Louis

first: Kia

middle: Marie

last: Barclay

email: kbarclay@wustl.edu, qingyunli@wustl.edu

state: MO

address: 4370 Duncan Ave

department: Neuroscience

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Assembly: mm10
Supplementary files format and content: Common delimited file (csv) containing all 2634 cells and mapped gene counts

molecule: total RNA

organism: Mus musculus

source_name: Corpus Callosum and Striatum

extract_protocol:
Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) gate were sorted into 96-well plates for library preparation.
Sorted microglia plates were prepared for scRNA-sequencing following the previously published Smart-seq2 protocol (Zhou et al 2019). Plates were thawed and primer annealing was performed at 72°C for 3 minutes.  Reverse transcription was performed by adding 6uL of reverse transcription mixture (95U SMARTScribe Reverse Transcriptase (100U/uL, Clontech 639538), 10U RNase inhibitor (40U/uL), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Rnase free HPLC purified) to each well (PCR protocol - at 42°C for 90 min, followed by 70°C, 5 min). DNA preamplification was done by adding 15 uL of PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/uL, New England BioLabs M0262S) to each well (PCR protocol - (1) 37°C 30 min; (2)95°C 3 min; (3) 23 cycles of 98°C 20 s, 67°C 15 s, 72°C 4 min; (4) 72°C 5 min). cDNA was cleaned using PCRClean DX beads (0.7:1 ratio, Aline C-1003-50) and resuspended in 20uL EB buffer. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6uL (1.2uL Tagment enzyme mix, 0.4uL cDNA) at 55°C, 10 min. To stop the reaction, neutralization buffer was added 0.4uL per well and incubated at room temperature for 5 min. Then 0.8uL Illumina 10-bp dual indexes (0.4uL each, 5uM) and 1.2uL PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72°C 3 min; (2) 95°C 30 s; (3) 10 cycles of 95°C 10 s, 55°C 30 s, 72°C 1 min; (4) 72°C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nova sequencing. To maximize PCR amplification efficiency for cuprizone demyelination samples, biotinylated-oligo-dT30VN oligo and biotinylated-TSO oligo were used in place of Oligo-dT30VN and TSO respectively, as described in an enhanced Smart-seq2 protocol (Gardeux et al 2022).

tag: tissue

value: Corpus Callosum and Striatum

tag: cell line

value: Isolated Microglia

tag: cell type

tag: condition

value: Demyelination

tag: age

value: 2 months

tag: tdtom

value: Neg


title: Cup.rep2.Neg.Plate2.D11


title: Cup.rep2.Neg.Plate1.H11


title: Cup.rep2.Neg.Plate2.A11


title: Cup.rep1.Neg.Plate1.C7


title: Cup.rep1.Neg.Plate1.E1


title: Cup.rep2.Neg.Plate2.B11


title: Cup.rep2.Neg.Plate1.C11


title: Cup.rep2.Neg.Plate2.G3


title: Cup.rep2.Neg.Plate1.A3


title: Cup.rep2.Neg.Plate1.F3


title: Cup.rep2.Neg.Plate2.C11


title: Cup.rep2.Neg.Plate2.F3


title: Cup.rep2.Neg.Plate2.E3


title: Cup.rep2.Neg.Plate1.D3


title: Cup.rep2.Neg.Plate2.D3


title: Cup.rep2.Neg.Plate1.B3


title: Cup.rep2.Neg.Plate2.A3


title: Cup.rep2.Neg.Plate2.B3


title: Cup.rep2.Neg.Plate1.A11


title: Cup.rep2.Neg.Plate1.H3


title: Cup.rep2.Neg.Plate1.E3


title: Cup.rep2.Neg.Plate1.C3


title: Cup.rep2.Neg.Plate2.G12


title: Cup.rep2.Neg.Plate2.H12


title: Cup.rep2.Neg.Plate1.G3


title: Cup.rep2.Neg.Plate2.C3


title: Cup.rep2.Neg.Plate2.H3


title: Cup.rep2.Neg.Plate1.A12


title: Cup.rep2.Neg.Plate1.B12


title: Cup.rep2.Neg.Plate1.E11


title: Cup.rep2.Neg.Plate1.D12


title: Cup.rep2.Neg.Plate2.E12


title: Cup.rep2.Neg.Plate2.F12


title: Cup.rep2.Neg.Plate1.H12


title: Cup.rep2.Neg.Plate2.A12


title: Cup.rep2.Neg.Plate1.G12


title: Cup.rep2.Neg.Plate2.C12


title: Cup.rep2.Neg.Plate1.E12


title: Cup.rep1.Neg.Plate1.A4


title: Cup.rep2.Neg.Plate1.C12


title: Cup.rep2.Neg.Plate2.B12


title: Cup.rep1.Neg.Plate1.H10


title: Cup.rep2.Neg.Plate1.F12


title: Cup.rep1.Neg.Plate1.F4


title: Cup.rep1.Neg.Plate1.H4


title: Cup.rep1.Neg.Plate1.B4


title: Cup.rep1.Neg.Plate1.E10


title: Cup.rep1.Neg.Plate1.D10


title: Cup.rep2.Neg.Plate2.D12


title: Cup.rep1.Neg.Plate1.F10


title: Cup.rep1.Neg.Plate1.G4


title: Cup.rep1.Neg.Plate1.C10


title: Cup.rep1.Neg.Plate1.A10


title: Cup.rep1.Neg.Plate1.B10


title: Cup.rep2.Neg.Plate2.H8


title: Cup.rep2.Neg.Plate2.G8


title: Cup.rep1.Neg.Plate1.E4


title: Cup.rep1.Neg.Plate1.D4


title: Cup.rep1.Neg.Plate1.C4


title: Cup.rep2.Neg.Plate1.B8


title: Cup.rep2.Neg.Plate1.D8


title: Cup.rep2.Neg.Plate2.F8


title: Cup.rep2.Neg.Plate1.F8


title: Cup.rep2.Neg.Plate2.E8


title: Cup.rep2.Neg.Plate1.A8


title: Cup.rep2.Neg.Plate2.D8


title: Cup.rep2.Neg.Plate1.H8


title: Cup.rep2.Neg.Plate2.C8


title: Cup.rep2.Neg.Plate1.E8


title: Cup.rep2.Neg.Plate2.B8


title: Cup.rep2.Neg.Plate1.G8


title: SVZ_Oligo_D24 pM [scNOME-seq]

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
single-cell NOMe-seq
meth_mfrac_promoter.csv.gz
meth_shrunkResid_promoter.csv.gz
meth_mfrac_VMR.csv.gz
meth_shrunkResid_VMR.csv.gz
meth_coverage_VMR.csv.gz
acc_mfrac_promoter.csv.gz
acc_shrunkResid_promoter.csv.gz
acc_mfrac_VMR.csv.gz
acc_shrunkResid_VMR.csv.gz

library_source: genomic

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

molecule: genomic DNA

source_name: striatum & ventricular-subventricular zone

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

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

value: oligodendrocyte

tag: genotype

value: TiCY

tag: treatment

value: naive


title: SVZ_Oligo_E23 pM [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: SVZ_Oligo_F24 pM [scNOME-seq]


title: SVZ_Oligo_I23 pM [scNOME-seq]


title: SVZ_Oligo_H24 pM [scNOME-seq]

value: vSVZ astrocyte


title: SVZ_Oligo_E24 pM [scNOME-seq]


title: SVZ_Oligo_I24 pM [scNOME-seq]


title: Cup.rep2.Neg.Plate1.C8


title: Cup.rep1.Neg.Plate1.G9


title: SVZ_Oligo_G24 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.H9


title: Cup.rep1.Neg.Plate1.A3


title: SVZ_Oligo_C24 pM [scNOME-seq]


title: Cup.rep2.Neg.Plate2.A8


title: SVZ_Oligo_C23 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.G10


title: Cup.rep1.Neg.Plate1.D3


title: SVZ_Oligo_D23 pM [scNOME-seq]


title: SVZ_Oligo_B24 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.B3


title: SVZ_Oligo_A24 pM [scNOME-seq]


title: SVZ_Oligo_B23 pM [scNOME-seq]


title: SVZ_Glast_I8 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.D9


title: Cup.rep1.Neg.Plate1.F9


title: SVZ_Glast_I6 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.H3


title: SVZ_Glast_I3 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.B9


title: Cup.rep1.Neg.Plate1.A9


title: Cup.rep1.Neg.Plate1.G3


title: SVZ_Glast_I4 pM [scNOME-seq]


title: SVZ_Glast_I22 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.C9


title: SVZ_Glast_I5 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B10

value: Pos


title: SVZ_Glast_I20 pM [scNOME-seq]


title: SVZ_Glast_I21 pM [scNOME-seq]


title: SVZ_Glast_I2 pM [scNOME-seq]

value: aNSC


title: Cup.rep2.Neg.Plate2.E1


title: Cup.rep1.Neg.Plate1.F3


title: Cup.rep1.Neg.Plate1.C3


title: SVZ_Glast_I19 pM [scNOME-seq]


title: SVZ_Glast_I18 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B10


title: Cup.rep1.Pos.Plate2.D10


title: Cup.rep1.Pos.Plate1.C10


title: Cup.rep1.Neg.Plate1.E9


title: SVZ_Glast_I17 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F10


title: SVZ_Glast_I16 pM [scNOME-seq]

value: neuroblast


title: SVZ_Glast_I7 pM [scNOME-seq]


title: Cup.rep1.Neg.Plate1.E3


title: SVZ_Glast_I15 pM [scNOME-seq]

value: TAP


title: Cup.rep1.Pos.Plate1.D10


title: SVZ_Glast_I14 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F10


title: SVZ_Glast_I13 pM [scNOME-seq]


title: SVZ_Glast_I12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.C10


title: SVZ_Glast_I11 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.G10


title: SVZ_Glast_I10 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G10


title: Cup.rep1.Pos.Plate2.A10


title: SVZ_Glast_H9 pM [scNOME-seq]


title: SVZ_Glast_I1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A10


title: SVZ_Glast_H8 pM [scNOME-seq]


title: SVZ_Glast_H7 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H10


title: Cup.rep2.Pos.Plate2.B7


title: SVZ_Glast_H5 pM [scNOME-seq]


title: SVZ_Glast_H6 pM [scNOME-seq]


title: SVZ_Glast_H22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B7


title: Cup.rep2.Pos.Plate1.C7


title: Cup.rep1.Pos.Plate1.E10


title: SVZ_Glast_H3 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.E10


title: Cup.rep2.Pos.Plate1.F7


title: Cup.rep1.Pos.Plate1.H10


title: SVZ_Glast_H4 pM [scNOME-seq]


title: SVZ_Glast_H20 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D7


title: Cup.rep2.Pos.Plate1.D7


title: SVZ_Glast_H21 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F7


title: SVZ_Glast_H19 pM [scNOME-seq]


title: SVZ_Glast_H18 pM [scNOME-seq]


title: SVZ_Glast_H16 pM [scNOME-seq]


title: SVZ_Glast_H14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G7


title: Cup.rep2.Pos.Plate1.H7


title: Cup.rep2.Pos.Plate1.G7


title: Cup.rep2.Pos.Plate2.C7


title: SVZ_Glast_H17 pM [scNOME-seq]


title: SVZ_Glast_H13 pM [scNOME-seq]


title: SVZ_Glast_H2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A7


title: Cup.rep2.Pos.Plate2.E7


title: Cup.rep2.Pos.Plate1.A7


title: SVZ_Glast_H12 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H7


title: SVZ_Glast_H11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B6


title: SVZ_Glast_H1 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D6


title: Cup.rep2.Pos.Plate1.C6


title: SVZ_Glast_H10 pM [scNOME-seq]


title: SVZ_Glast_G9 pM [scNOME-seq]


title: SVZ_Glast_G5 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B6


title: SVZ_Glast_G6 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F6


title: SVZ_Glast_H15 pM [scNOME-seq]


title: SVZ_Glast_G4 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D6


title: Cup.rep2.Pos.Plate2.F6


title: SVZ_Glast_G3 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E6


title: Cup.rep2.Pos.Plate1.H6


title: SVZ_Glast_G20 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C6


title: SVZ_Glast_G21 pM [scNOME-seq]


title: SVZ_Glast_G2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G6


title: SVZ_Glast_G19 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G6


title: Cup.rep2.Pos.Plate2.E6


title: Cup.rep2.Pos.Plate2.A6


title: SVZ_Glast_G17 pM [scNOME-seq]


title: SVZ_Glast_G16 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A6


title: SVZ_Glast_G18 pM [scNOME-seq]


title: SVZ_Glast_G15 pM [scNOME-seq]


title: SVZ_Glast_G14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E7


title: SVZ_Glast_G12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B8


title: Cup.rep1.Pos.Plate2.D8


title: SVZ_Glast_G13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.C8


title: SVZ_Glast_G11 pM [scNOME-seq]


title: SVZ_Glast_G10 pM [scNOME-seq]


title: SVZ_Glast_G22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H6


title: SVZ_Glast_G1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D8


title: SVZ_Glast_F9 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B8


title: SVZ_Glast_F8 pM [scNOME-seq]


title: SVZ_Glast_F6 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H8


title: SVZ_Glast_F7 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.C8


title: Cup.rep1.Pos.Plate1.G8


title: Cup.rep1.Pos.Plate2.A8


title: SVZ_Glast_F4 pM [scNOME-seq]


title: SVZ_Glast_F5 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A8


title: SVZ_Glast_F3 pM [scNOME-seq]


title: SVZ_Glast_F21 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.E8


title: SVZ_Glast_F20 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F8


title: Cup.rep1.Pos.Plate1.E8


title: SVZ_Glast_F17 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D3


title: Cup.rep1.Pos.Plate2.F8


title: Cup.rep1.Pos.Plate2.B3


title: SVZ_Glast_F16 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.C3


title: SVZ_Glast_F18 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B3


title: Cup.rep1.Pos.Plate1.F3


title: SVZ_Glast_F14 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D3


title: SVZ_Glast_F13 pM [scNOME-seq]


title: SVZ_Glast_F22 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H8


title: SVZ_Glast_F12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F3


title: SVZ_Glast_F19 pM [scNOME-seq]


title: SVZ_Glast_F11 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H3


title: Cup.rep1.Pos.Plate2.G3


title: SVZ_Glast_E9 pM [scNOME-seq]


title: SVZ_Glast_F10 pM [scNOME-seq]


title: SVZ_Glast_F1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G3


title: SVZ_Glast_E8 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A3


title: SVZ_Glast_F15 pM [scNOME-seq]


title: SVZ_Glast_E7 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.G8


title: SVZ_Glast_E6 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.E3


title: SVZ_Glast_E5 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H3


title: SVZ_Glast_E3 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D11


title: Cup.rep1.Pos.Plate2.B11


title: Cup.rep1.Pos.Plate1.E3


title: Cup.rep1.Pos.Plate1.F11


title: Cup.rep1.Pos.Plate2.C3


title: SVZ_Glast_E2 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.C11


title: Cup.rep1.Pos.Plate1.B11


title: SVZ_Glast_E19 pM [scNOME-seq]


title: SVZ_Glast_E20 pM [scNOME-seq]


title: SVZ_Glast_E21 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D11


title: SVZ_Glast_E17 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E11


title: Cup.rep1.Pos.Plate1.A3


title: Cup.rep1.Pos.Plate2.C11


title: SVZ_Glast_E16 pM [scNOME-seq]


title: SVZ_Glast_E15 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F11


title: SVZ_Glast_E12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H11


title: Cup.rep1.Pos.Plate1.G11


title: SVZ_Glast_E14 pM [scNOME-seq]


title: SVZ_Glast_E22 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.E11


title: Cup.rep1.Pos.Plate2.G11


title: Cup.rep1.Pos.Plate1.A11


title: SVZ_Glast_E11 pM [scNOME-seq]


title: SVZ_Glast_E10 pM [scNOME-seq]


title: SVZ_Glast_D9 pM [scNOME-seq]


title: SVZ_Glast_E18 pM [scNOME-seq]


title: SVZ_Glast_D8 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A11


title: SVZ_Glast_D7 pM [scNOME-seq]


title: SVZ_Glast_D6 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B8


title: Cup.rep2.Pos.Plate2.D8


title: Cup.rep2.Pos.Plate1.C8


title: Cup.rep2.Pos.Plate1.B8


title: Cup.rep2.Pos.Plate1.F8


title: SVZ_Glast_D4 pM [scNOME-seq]


title: SVZ_Glast_E13 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D8


title: SVZ_Glast_D3 pM [scNOME-seq]


title: SVZ_Glast_D22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E8


title: SVZ_Glast_D20 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C8


title: Cup.rep2.Pos.Plate2.F8


title: Cup.rep1.Pos.Plate2.H11


title: SVZ_Glast_D2 pM [scNOME-seq]


title: SVZ_Glast_D17 pM [scNOME-seq]


title: SVZ_Glast_D5 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G8


title: SVZ_Glast_D19 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A8


title: Cup.rep2.Pos.Plate1.H8


title: Cup.rep2.Pos.Plate2.E8


title: SVZ_Glast_D15 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G8


title: SVZ_Glast_D13 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H8


title: Cup.rep2.Pos.Plate2.B11


title: SVZ_Glast_D12 pM [scNOME-seq]


title: SVZ_Glast_D21 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D11


title: SVZ_Glast_D10 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B11


title: Cup.rep2.Pos.Plate1.C11


title: SVZ_Glast_D1 pM [scNOME-seq]


title: SVZ_Glast_C9 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D11


title: SVZ_Glast_C8 pM [scNOME-seq]


title: SVZ_Glast_C7 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F11


title: SVZ_Glast_D16 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A8


title: Cup.rep2.Pos.Plate1.G11


title: SVZ_Glast_D14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E11


title: Cup.rep2.Pos.Plate2.G11


title: SVZ_Glast_C5 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C11


title: Cup.rep2.Pos.Plate1.H11


title: SVZ_Glast_C3 pM [scNOME-seq]


title: SVZ_Glast_C4 pM [scNOME-seq]


title: SVZ_Glast_C21 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A11


title: SVZ_Glast_C2 pM [scNOME-seq]


title: SVZ_Glast_C22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E11


title: Cup.rep2.Pos.Plate2.H11


title: SVZ_Glast_C20 pM [scNOME-seq]


title: SVZ_Glast_C18 pM [scNOME-seq]


title: SVZ_Glast_C19 pM [scNOME-seq]


title: SVZ_Glast_C17 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B9


title: Cup.rep2.Pos.Plate2.D9


title: Cup.rep2.Pos.Plate1.B9


title: SVZ_Glast_C16 pM [scNOME-seq]


title: SVZ_Glast_C15 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F11


title: Cup.rep2.Pos.Plate1.C9


title: SVZ_Glast_C6 pM [scNOME-seq]


title: SVZ_Glast_D11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A11


title: SVZ_Glast_C14 pM [scNOME-seq]


title: SVZ_Glast_C13 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E9


title: Cup.rep2.Pos.Plate1.F9


title: SVZ_Glast_C10 pM [scNOME-seq]


title: SVZ_Glast_C12 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F9


title: SVZ_Glast_C11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C9


title: SVZ_Glast_B8 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G9


title: SVZ_Glast_B7 pM [scNOME-seq]


title: SVZ_Glast_C1 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A9


title: Cup.rep2.Pos.Plate1.H9


title: SVZ_Glast_B6 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G9


title: Cup.rep2.Pos.Plate1.A9


title: SVZ_Glast_B5 pM [scNOME-seq]


title: SVZ_Glast_B4 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H9


title: SVZ_Glast_B22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E9


title: Cup.rep1.Pos.Plate2.B6


title: SVZ_Glast_B21 pM [scNOME-seq]


title: SVZ_Glast_B3 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D6


title: Cup.rep1.Pos.Plate1.C6


title: SVZ_Glast_B20 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B6


title: SVZ_Glast_B2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D9


title: Cup.rep1.Pos.Plate2.C6


title: Cup.rep1.Pos.Plate2.F6


title: Cup.rep1.Pos.Plate1.F6


title: SVZ_Glast_B18 pM [scNOME-seq]


title: SVZ_Glast_B17 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D6


title: SVZ_Glast_B16 pM [scNOME-seq]


title: SVZ_Glast_B10 pM [scNOME-seq]


title: SVZ_Glast_B12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.G6


title: SVZ_Glast_B15 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A6


title: Cup.rep1.Pos.Plate2.E6


title: SVZ_Glast_B13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H6


title: Cup.rep1.Pos.Plate1.G6


title: Cup.rep1.Pos.Plate1.E6


title: SVZ_Glast_A9 pM [scNOME-seq]


title: SVZ_Glast_B1 pM [scNOME-seq]


title: SVZ_Glast_B14 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D7


title: Cup.rep1.Pos.Plate1.A6


title: SVZ_Glast_A7 pM [scNOME-seq]


title: SVZ_Glast_A4 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H6


title: SVZ_Glast_A22 pM [scNOME-seq]


title: SVZ_Glast_A21 pM [scNOME-seq]


title: SVZ_Glast_A3 pM [scNOME-seq]


title: SVZ_Glast_A5 pM [scNOME-seq]


title: SVZ_Glast_A6 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B7


title: Cup.rep1.Pos.Plate1.D7


title: Cup.rep1.Pos.Plate1.C7


title: SVZ_Glast_A18 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E7


title: Cup.rep1.Pos.Plate1.F7


title: Cup.rep1.Pos.Plate2.G7


title: SVZ_Glast_A20 pM [scNOME-seq]


title: SVZ_Glast_A8 pM [scNOME-seq]


title: SVZ_Glast_A2 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F7


title: SVZ_Glast_A19 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H7


title: SVZ_Glast_A17 pM [scNOME-seq]


title: SVZ_Glast_A16 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G7


title: Cup.rep1.Pos.Plate2.A7


title: Cup.rep1.Pos.Plate1.B7


title: Cup.rep1.Pos.Plate2.E7


title: SVZ_Glast_A14 pM [scNOME-seq]


title: SVZ_Glast_A12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A7


title: SVZ_Glast_A13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H7


title: Cup.rep2.Pos.Plate1.C3


title: SVZ_Glast_A1 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D3


title: Cup.rep1.Pos.Plate2.C7


title: Str_Glast_P9 pM [scNOME-seq]

value: astrocyte (striatum)


title: Cup.rep2.Pos.Plate1.B3


title: SVZ_Glast_A11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F3


title: Cup.rep2.Pos.Plate2.B3


title: Str_Glast_P8 pM [scNOME-seq]


title: Str_Glast_P4 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D3


title: Cup.rep2.Pos.Plate1.E3


title: Cup.rep2.Pos.Plate2.F3


title: Str_Glast_P23 pM [scNOME-seq]


title: SVZ_Glast_A15 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C3


title: Str_Glast_P7 pM [scNOME-seq]


title: Str_Glast_P20 pM [scNOME-seq]


title: Str_Glast_P21 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G3


title: Str_Glast_P2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.H3


title: Str_Glast_P18 pM [scNOME-seq]


title: Str_Glast_P17 pM [scNOME-seq]


title: SVZ_Glast_A10 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A3


title: Cup.rep2.Pos.Plate1.G3


title: Cup.rep2.Pos.Plate2.E3


title: Str_Glast_P16 pM [scNOME-seq]


title: Str_Glast_P14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A3


title: Str_Glast_P13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B12


title: Str_Glast_P11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H3


title: Cup.rep1.Pos.Plate1.C12


title: Cup.rep1.Pos.Plate2.D12


title: Str_Glast_P1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B12


title: Str_Glast_O8 pM [scNOME-seq]


title: Str_Glast_O9 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F12


title: Cup.rep1.Pos.Plate1.D12


title: Str_Glast_O5 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F12


title: Str_Glast_O6 pM [scNOME-seq]


title: Str_Glast_O4 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E12


title: Cup.rep1.Pos.Plate2.C12


title: Cup.rep1.Pos.Plate2.G12


title: Str_Glast_O20 pM [scNOME-seq]


title: Str_Glast_O2 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G12


title: Cup.rep1.Pos.Plate1.H12


title: Str_Glast_O18 pM [scNOME-seq]


title: Str_Glast_O17 pM [scNOME-seq]


title: Str_Glast_O13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A12


title: Cup.rep1.Pos.Plate2.E12


title: Cup.rep1.Pos.Plate2.H12


title: Str_Glast_O7 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B5


title: Str_Glast_O11 pM [scNOME-seq]


title: Str_Glast_O12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D5


title: Str_Glast_O10 pM [scNOME-seq]


title: Str_Glast_O1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.C5


title: Str_Glast_N8 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B5


title: Str_Glast_N7 pM [scNOME-seq]


title: Str_Glast_O3 pM [scNOME-seq]


title: Str_Glast_N9 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F5


title: Cup.rep1.Pos.Plate2.F5


title: Str_Glast_N5 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D5


title: Cup.rep1.Pos.Plate2.C5


title: Str_Glast_N3 pM [scNOME-seq]


title: Str_Glast_N4 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A12


title: Str_Glast_N24 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E5


title: Cup.rep1.Pos.Plate2.G5


title: Cup.rep1.Pos.Plate1.G5


title: Cup.rep1.Pos.Plate2.A5


title: Cup.rep1.Pos.Plate1.H5


title: Cup.rep1.Pos.Plate2.E5


title: Str_Glast_N21 pM [scNOME-seq]


title: Str_Glast_N23 pM [scNOME-seq]


title: Str_Glast_N22 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H5


title: Cup.rep1.Pos.Plate1.A5


title: Str_Glast_N6 pM [scNOME-seq]


title: Str_Glast_N20 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D9


title: Cup.rep1.Pos.Plate1.C9


title: Cup.rep1.Pos.Plate1.B9


title: Str_Glast_N16 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F9


title: Str_Glast_N14 pM [scNOME-seq]


title: Str_Glast_N13 pM [scNOME-seq]


title: Str_Glast_N17 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D9


title: Cup.rep1.Pos.Plate1.E9


title: Str_Glast_N12 pM [scNOME-seq]


title: Str_Glast_N10 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.C9


title: Str_Glast_N19 pM [scNOME-seq]


title: Str_Glast_N1 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G9


title: Str_Glast_M8 pM [scNOME-seq]


title: Str_Glast_N18 pM [scNOME-seq]


title: Str_Glast_M9 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B9


title: Cup.rep1.Pos.Plate2.G9


title: Str_Glast_M7 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A9


title: Cup.rep1.Pos.Plate2.E9


title: Str_Glast_M6 pM [scNOME-seq]


title: Str_Glast_O22 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A9


title: Str_Glast_N15 pM [scNOME-seq]


title: Str_Glast_M4 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H9


title: Cup.rep2.Pos.Plate2.B4


title: Str_Glast_M3 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D4


title: Cup.rep1.Pos.Plate2.F9


title: Str_Glast_N11 pM [scNOME-seq]


title: Str_Glast_M24 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.C4


title: Str_Glast_M23 pM [scNOME-seq]


title: Str_Glast_M22 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H9


title: Str_Glast_M21 pM [scNOME-seq]


title: Str_Glast_M20 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F4


title: Str_Glast_M5 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D4


title: Cup.rep2.Pos.Plate1.E4


title: Cup.rep2.Pos.Plate2.C4


title: Cup.rep2.Pos.Plate2.F4


title: Str_Glast_M17 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G4


title: Str_Glast_M16 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.H4


title: Cup.rep2.Pos.Plate1.G4


title: Str_Glast_M12 pM [scNOME-seq]


title: Str_Glast_M14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E4


title: Str_Glast_M11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H4


title: Cup.rep2.Pos.Plate1.A4


title: Str_Glast_M10 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B5


title: Cup.rep2.Pos.Plate1.B4


title: Str_Glast_M1 pM [scNOME-seq]


title: Str_Glast_L9 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D5


title: Str_Glast_M2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.C5


title: Str_Glast_M18 pM [scNOME-seq]


title: Str_Glast_L7 pM [scNOME-seq]


title: Str_Glast_L8 pM [scNOME-seq]


title: Str_Glast_M15 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B5


title: Str_Glast_M19 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F5


title: Str_Glast_L4 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F5


title: Cup.rep2.Pos.Plate1.E5


title: Str_Glast_L24 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D5


title: Str_Glast_L6 pM [scNOME-seq]


title: Str_Glast_L22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C5


title: Str_Glast_L21 pM [scNOME-seq]


title: Str_Glast_L2 pM [scNOME-seq]


title: Str_Glast_L19 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G5


title: Cup.rep2.Pos.Plate2.A5


title: Str_Glast_L17 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A5


title: Str_Glast_L15 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H5


title: Str_Glast_L14 pM [scNOME-seq]


title: Str_Glast_L3 pM [scNOME-seq]


title: Str_Glast_L13 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B1


title: Cup.rep2.Pos.Plate2.G5


title: Str_Glast_L12 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.C1


title: Cup.rep2.Pos.Plate1.H5


title: Str_Glast_L1 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D1


title: Str_Glast_L10 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E5


title: Cup.rep2.Pos.Plate1.B1


title: Str_Glast_L16 pM [scNOME-seq]


title: Str_Glast_K9 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F1


title: Cup.rep2.Pos.Plate1.D1


title: Cup.rep2.Pos.Plate2.C1


title: Str_Glast_K4 pM [scNOME-seq]


title: Str_Glast_K5 pM [scNOME-seq]


title: Str_Glast_K3 pM [scNOME-seq]


title: Str_Glast_K24 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G1


title: Str_Glast_K7 pM [scNOME-seq]


title: Str_Glast_K23 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G1


title: Str_Glast_K22 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A1


title: Str_Glast_K21 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F1


title: Cup.rep2.Pos.Plate2.E1


title: Str_Glast_K19 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A1


title: Str_Glast_K17 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B2


title: Str_Glast_K2 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H1


title: Cup.rep2.Pos.Plate2.D2


title: Cup.rep2.Pos.Plate1.F2


title: Cup.rep2.Pos.Plate1.C2


title: Str_Glast_K16 pM [scNOME-seq]


title: Str_Glast_K14 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F2


title: Str_Glast_K15 pM [scNOME-seq]


title: Str_Glast_K12 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B2


title: Str_Glast_K11 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D2


title: Str_Glast_K13 pM [scNOME-seq]


title: Str_Glast_K10 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A4


title: Cup.rep2.Pos.Plate1.E2


title: Cup.rep2.Pos.Plate1.H1


title: Cup.rep2.Pos.Plate2.C2


title: Str_Glast_K20 pM [scNOME-seq]


title: Str_Glast_K1 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G2


title: Str_Glast_J9 pM [scNOME-seq]


title: Str_Glast_J6 pM [scNOME-seq]


title: Str_Glast_J5 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate1.H2


title: Str_Glast_J23 pM [scNOME-seq]


title: Str_Glast_J4 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E2


title: Cup.rep2.Pos.Plate1.G2


title: Cup.rep2.Pos.Plate2.A2


title: Cup.rep1.Pos.Plate2.B1


title: Str_Glast_J20 pM [scNOME-seq]


title: Str_Glast_J19 pM [scNOME-seq]


title: Str_Glast_J18 pM [scNOME-seq]


title: Cup.rep2.Pos.Plate2.H2


title: Str_Glast_J17 pM [scNOME-seq]


title: Str_Glast_J15 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D1


title: Cup.rep1.Pos.Plate1.C1


title: Str_Glast_J13 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B1


title: Cup.rep1.Pos.Plate1.F1


title: Str_Glast_J12 pM [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D1


title: Str_Glast_GFP+_D9 pL [scNOME-seq]

source_name: cerebral cortex & striatum

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: Cup.rep1.Pos.Plate2.F1

value: Corpus Callosum and Striatum


title: Str_Glast_GFP+_D8 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E1

value: Isolated Microglia


title: Cup.rep2.Pos.Plate1.A2

value: Demyelination


title: Cup.rep1.Pos.Plate2.C1

value: 2 months


title: Str_Glast_GFP+_D7 pL [scNOME-seq]


title: Str_Glast_J22 pM [scNOME-seq]


title: Str_Glast_GFP+_D6 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H1


title: Str_Glast_GFP+_D11 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E1


title: Cup.rep1.Pos.Plate1.G1


title: Cup.rep1.Pos.Plate2.G1


title: Str_Glast_GFP+_C9 pL [scNOME-seq]


title: Str_Glast_GFP+_C8 pL [scNOME-seq]


title: Str_Glast_GFP+_C7 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H1


title: Cup.rep1.Pos.Plate2.E1


title: Cup.rep2.Pos.Plate2.B10


title: Str_Glast_GFP+_D1 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.A1


title: Str_Glast_GFP+_C4 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.D10


title: Str_Glast_GFP+_C3 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A1


title: Cup.rep2.Pos.Plate1.C10


title: Cup.rep2.Pos.Plate1.B10


title: Str_Glast_GFP+_C2 pL [scNOME-seq]


title: Str_Glast_GFP+_C6 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.F10


title: Str_Glast_GFP+_C11 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F10


title: Str_Glast_GFP+_C10 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.E10


title: Str_Glast_GFP+_B9 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D10


title: Str_Glast_GFP+_D10 pL [scNOME-seq]


title: Str_Glast_GFP+_B8 pL [scNOME-seq]


title: Str_Glast_GFP+_B5 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.G10


title: Str_Glast_GFP+_B6 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.C10


title: Str_Glast_GFP+_B3 pL [scNOME-seq]


title: Str_Glast_GFP+_B2 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E10


title: Str_Glast_GFP+_B4 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.H10


title: Cup.rep2.Pos.Plate2.A10


title: Str_Glast_GFP+_B10 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B2


title: Cup.rep2.Pos.Plate2.H10


title: Str_Glast_GFP+_B1 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.A10


title: Str_Glast_GFP+_A9 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D2


title: Str_Glast_GFP+_A5 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.B2


title: Cup.rep1.Pos.Plate1.C2


title: Str_Glast_GFP+_A3 pL [scNOME-seq]


title: Str_Glast_GFP+_A4 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.F2


title: Str_Glast_GFP+_A12 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D2


title: Cup.rep1.Pos.Plate1.F2


title: Str_Glast_GFP+_A11 pL [scNOME-seq]


title: Ctx_Glast_P10 pL [scNOME-seq]

value: astrocyte (cortex)


title: Cup.rep2.Pos.Plate1.G10


title: Str_Glast_GFP+_A10 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E2


title: Ctx_Glast_GFP+_L8 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.C2


title: Ctx_Glast_GFP+_L7 pL [scNOME-seq]


title: Str_Glast_GFP+_A8 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.G2


title: Cup.rep1.Pos.Plate1.H2


title: Ctx_Glast_GFP+_L3 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.G2


title: Cup.rep1.Pos.Plate2.E2


title: Ctx_Glast_GFP+_L1 pL [scNOME-seq]


title: Ctx_Glast_GFP+_L4 pL [scNOME-seq]


title: Ctx_Glast_GFP+_L11 pL [scNOME-seq]


title: Ctx_Glast_GFP+_L10 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A2


title: Cup.rep1.Pos.Plate1.A2


title: Ctx_Glast_GFP+_K8 pL [scNOME-seq]


title: Ctx_Glast_GFP+_L2 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.D4


title: Cup.rep1.Pos.Plate2.H2


title: Ctx_Glast_GFP+_K7 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.C4


title: Cup.rep1.Pos.Plate1.B4


title: Ctx_Glast_GFP+_K4 pL [scNOME-seq]


title: Ctx_Glast_GFP+_K2 pL [scNOME-seq]


title: Ctx_Glast_GFP+_K6 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.F4


title: Ctx_Glast_GFP+_K3 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.D4


title: Cup.rep1.Pos.Plate2.F4


title: Ctx_Glast_GFP+_K12 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.E4


title: Cup.rep1.Pos.Plate2.C4


title: Ctx_Glast_GFP+_J5 pL [scNOME-seq]


title: Ctx_Glast_GFP+_J2 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.B4


title: Cup.rep1.Pos.Plate1.G4


title: Ctx_Glast_GFP+_J3 pL [scNOME-seq]


title: Ctx_Glast_GFP+_K1 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.E4


title: Ctx_Glast_GFP+_J10 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.A4


title: Ctx_Glast_GFP+_J7 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate1.H4


title: Cup.rep1.Pos.Plate1.A4


title: Ctx_Glast_GFP+_I7 pL [scNOME-seq]


title: Ctx_Glast_GFP+_I8 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.H4


title: Ctx_Glast_GFP+_I6 pL [scNOME-seq]


title: Ctx_Glast_GFP+_K10 pL [scNOME-seq]


title: Ctx_Glast_GFP+_I4 pL [scNOME-seq]


title: Ctx_Glast_GFP+_I5 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.B12


title: Cup.rep2.Pos.Plate1.C12


title: Ctx_Glast_GFP+_I11 pL [scNOME-seq]


title: Cup.rep1.Pos.Plate2.G4


title: Cup.rep2.Pos.Plate2.D12


title: Ctx_Glast_GFP+_I10 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate1.D12


title: Ctx_Glast_GFP+_I1 pL [scNOME-seq]


title: Cup.rep2.Pos.Plate2.B12


title: Cup.rep2.Pos.Plate1.F12


title: Cup.rep2.Pos.Plate1.E12


title: Cup.rep2.Pos.Plate2.C12


title: SVZ_Glast_L9_naive pJ [scNOME-seq]

value: IFN(A/G)R KO


title: Cup.rep2.Pos.Plate2.G12


title: SVZ_Glast_L8_naive pJ [scNOME-seq]


title: SVZ_Glast_L18_naive pJ [scNOME-seq]


title: Cup.rep2.Pos.Plate2.E12


title: SVZ_Glast_L7_naive pJ [scNOME-seq]


title: SVZ_Glast_L13_naive pJ [scNOME-seq]


title: Cup.rep2.Pos.Plate1.G12


title: Cup.rep2.Pos.Plate1.A12


title: SVZ_Glast_L16_naive pJ [scNOME-seq]


title: Cup.rep2.Pos.Plate2.A12


title: Cup.rep2.Pos.Plate1.H12


title: Cup.rep2.Pos.Plate2.H12


title: CupR.rep1.Pos.Plate2.H9

value: Remyelination


title: SVZ_Glast_L11_naive pJ [scNOME-seq]

value: naive


title: Ctx_Glast_GFP+_I12 pL [scNOME-seq]


title: SVZ_Glast_L17_naive pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_L12_naive pJ [scNOME-seq]

value: vSVZ astrocyte


title: CupR.rep1.Pos.Plate2.H8

value: Pos


title: SVZ_Glast_L10_naive pJ [scNOME-seq]


title: SVZ_Glast_K9_naive pJ [scNOME-seq]


title: Cup.rep2.Pos.Plate2.F12


title: SVZ_Glast_K7_naive pJ [scNOME-seq]


title: SVZ_Glast_K8_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H5


title: SVZ_Glast_K18_naive pJ [scNOME-seq]


title: SVZ_Glast_L14_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H4


title: CupR.rep1.Pos.Plate2.H2


title: SVZ_Glast_K17_naive pJ [scNOME-seq]


title: SVZ_Glast_K15_naive pJ [scNOME-seq]


title: SVZ_Glast_K16_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H12


title: CupR.rep1.Pos.Plate2.H11


title: SVZ_Glast_K14_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H10


title: SVZ_Glast_K13_naive pJ [scNOME-seq]


title: SVZ_Glast_K11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H7


title: CupR.rep1.Pos.Plate2.G9


title: CupR.rep1.Pos.Plate2.G7


title: CupR.rep1.Pos.Plate2.G8


title: SVZ_Glast_J9_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.G6


title: SVZ_Glast_J18_naive pJ [scNOME-seq]


title: SVZ_Glast_K10_naive pJ [scNOME-seq]


title: SVZ_Glast_J8_naive pJ [scNOME-seq]

value: aNSC


title: CupR.rep1.Pos.Plate2.H6


title: CupR.rep1.Pos.Plate2.G5


title: CupR.rep1.Pos.Plate2.G4


title: CupR.rep1.Pos.Plate2.H3


title: SVZ_Glast_J17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.G3


title: SVZ_Glast_J15_naive pJ [scNOME-seq]


title: SVZ_Glast_K12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.H1


title: CupR.rep1.Pos.Plate2.G11


title: SVZ_Glast_J12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.G10


title: SVZ_Glast_I9_naive pJ [scNOME-seq]


title: SVZ_Glast_J11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.F8


title: CupR.rep1.Pos.Plate2.F9


title: SVZ_Glast_I7_naive pJ [scNOME-seq]


title: SVZ_Glast_I18_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.F7


title: SVZ_Glast_I8_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.F5


title: SVZ_Glast_I17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.F6


title: SVZ_Glast_J16_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.F3


title: CupR.rep1.Pos.Plate2.F4


title: SVZ_Glast_I16_naive pJ [scNOME-seq]


title: SVZ_Glast_I15_naive pJ [scNOME-seq]

value: neuroblast


title: SVZ_Glast_I14_naive pJ [scNOME-seq]


title: SVZ_Glast_J14_naive pJ [scNOME-seq]

value: TAP


title: CupR.rep1.Pos.Plate2.F2


title: CupR.rep1.Pos.Plate2.G2


title: CupR.rep1.Pos.Plate2.F12


title: SVZ_Glast_J13_naive pJ [scNOME-seq]


title: SVZ_Glast_I13_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.G12


title: CupR.rep1.Pos.Plate2.G1


title: CupR.rep1.Pos.Plate2.F10


title: CupR.rep1.Pos.Plate2.F11


title: SVZ_Glast_I10_naive pJ [scNOME-seq]


title: SVZ_Glast_I12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E9


title: SVZ_Glast_H9_naive pJ [scNOME-seq]


title: SVZ_Glast_H18_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E7


title: CupR.rep1.Pos.Plate2.E8


title: SVZ_Glast_H17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E5


title: SVZ_Glast_H16_naive pJ [scNOME-seq]


title: SVZ_Glast_H14_naive pJ [scNOME-seq]


title: SVZ_Glast_H15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E6


title: SVZ_Glast_I11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E2


title: SVZ_Glast_H13_naive pJ [scNOME-seq]


title: SVZ_Glast_H12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E11


title: SVZ_Glast_H10_naive pJ [scNOME-seq]


title: SVZ_Glast_G9_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E3


title: SVZ_Glast_H11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.E10


title: CupR.rep1.Pos.Plate2.F1


title: CupR.rep1.Pos.Plate2.D8


title: CupR.rep1.Pos.Plate2.D9


title: CupR.rep1.Pos.Plate2.E1


title: SVZ_Glast_H7_naive pJ [scNOME-seq]


title: SVZ_Glast_G18_naive pJ [scNOME-seq]


title: SVZ_Glast_G16_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.D7


title: CupR.rep1.Pos.Plate2.E4


title: CupR.rep1.Pos.Plate2.D6


title: SVZ_Glast_G13_naive pJ [scNOME-seq]


title: SVZ_Glast_G12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.D5


title: CupR.rep1.Pos.Plate2.D4


title: CupR.rep1.Pos.Plate2.E12


title: SVZ_Glast_G11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.D3


title: SVZ_Glast_F9_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.D12


title: CupR.rep1.Pos.Plate2.D11


title: CupR.rep1.Pos.Plate2.D2


title: SVZ_Glast_G17_naive pJ [scNOME-seq]


title: SVZ_Glast_F8_naive pJ [scNOME-seq]


title: SVZ_Glast_F7_naive pJ [scNOME-seq]


title: SVZ_Glast_F17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C8


title: SVZ_Glast_F15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C7


title: CupR.rep1.Pos.Plate2.D10


title: CupR.rep1.Pos.Plate2.C9


title: CupR.rep1.Pos.Plate2.D1


title: SVZ_Glast_F16_naive pJ [scNOME-seq]


title: SVZ_Glast_F14_naive pJ [scNOME-seq]


title: SVZ_Glast_G15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C6


title: SVZ_Glast_F13_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C5


title: SVZ_Glast_F11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C3


title: CupR.rep1.Pos.Plate2.C4


title: SVZ_Glast_F10_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C2


title: SVZ_Glast_G10_naive pJ [scNOME-seq]


title: SVZ_Glast_E9_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C12


title: SVZ_Glast_E8_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C11


title: SVZ_Glast_E7_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.C10


title: CupR.rep1.Pos.Plate2.C1


title: CupR.rep1.Pos.Plate2.B8


title: SVZ_Glast_E18_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B9


title: SVZ_Glast_E16_naive pJ [scNOME-seq]


title: COX14 Mutant 4

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20
STAR version 2.5 was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCm38 version 101
Assembly: GRCm38 version 101
Supplementary files format and content: CSV file containing normalized counts

molecule: polyA RNA

source_name: Liver

extract_protocol:
cut a  small tissue of a frozen / fresh organ and transfer in to a 1,5 ml tube:  - under the hood add 500µl TROZOL , use a hand held homogenizer/potter until there are no tissue      chunks flying around      Info: blue Potter tip (single packaged) 2. drawer - Add 100µl chloroform, mix until cloudy by vortexing the sample for 15 sec (not less as 15sec!) Incubate sample for 3 min 28°C ( for cells sample 24°C) 300rpm 15min 12.000g 4°C  remove upper phase very carefully  into a 1,5ml Protein LB DNA/RNase free (Sarstedt Ref.: 72.706.000)         ca. 200µl supernatant - and throw away the rest (do not touch the middle phase)         keep chloroform for safety and dispose in special waste finally - Add 150µl isopropanol, mix samples gently by inversion several times Incubate for 10min 28°C ( for cells sample 24°C) 300rpm 10min 12.000g 4°C Decant supernatant Add 500µl 75% ETOH , and mix samples gently by inversion several times 5min 7500g 4°C Remove/ decant the supernatant completely , dry Cup wall by using paper, take care about the pellet      remove supernatant by using a pipette since it is loose. Dry Pellet 28°C for 10 – 15 min ( Pellet will become translucent from white). Resuspend pellet in Dnase, Rnase free water 25µl (10-50µl) – 25 ul than diluted to 125ul for Nanodrop Incubate for 10 min at 60°C Measure RNA concentration (Nanodrop) immediately or store at -80°C (directly -80°C without nitrogen)
RNA sequencing (RNA-seq) libraries were performed using 200 ng total RNA of a non-stranded mRNA Seq (TruSeq RNA Library Preparation, #RS-122–2001)

value: Liver

value: MUT


title: COX14 Mutant 3


title: COX14 Mutant 1


title: CupR.rep1.Pos.Plate2.B5


title: SVZ_Glast_F12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B6


title: SVZ_Glast_E17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B7


title: SVZ_Glast_E15_naive pJ [scNOME-seq]


title: COX14 Mutant 2


title: WT Control 4

value: WT


title: SVZ_Glast_E14_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B2

value: Corpus Callosum and Striatum


title: CupR.rep1.Pos.Plate2.B12

value: Isolated Microglia


title: CupR.rep1.Pos.Plate2.B3


title: WT Control 3


title: SVZ_Glast_E13_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B10


title: CupR.rep1.Pos.Plate2.B11


title: SVZ_Glast_E12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.B1


title: WT Control 1


title: CupR.rep1.Pos.Plate2.A9


title: CupR.rep1.Pos.Plate2.B4


title: SVZ_Glast_E11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.A8


title: CupR.rep1.Pos.Plate2.A7


title: SVZ_Glast_E10_naive pJ [scNOME-seq]


title: KO_USP44_H3K27Me3_Rep3

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

institute: Robert Bosch Center for Tumor Diseases

data_processing:
All steps were performed with default settings unless otherwise denoted
Sequence reads were trimmed with fastx_trimmer (fastx/0.0.14)
Trimmed sequence reads were mapped to mm10 using bowtie2/2.3.3.1 using very-sensitive end-to-end mode
Bigwig generation was performed using bamCoverage (deeptools/3.3.2) using minimum mapping quality of 2, normalized to 1x depth of coverage (reads per genomic content, RPGC), and PCR duplicates removed. All three replicates were merged with samtools merge (samtools/1.9)
Assembly: mm10
Supplementary files format and content: Normalized bigwigs files

source_name: MEF

growth_protocol: MEFs were derived from mixed 129xC57BL/6-strain of ES cells that were immortalized with SV40 large T antigen. USP44 null cells were generated from exon 1 removal. Lentiviral transduction with USP44 cDNA was used to generate resuce cell line. Cells were cultured in DMEM with 10% FBS.

extract_protocol:
MEFs were fixed in 1% formaldehyde in PBS for 20 min and quenched with 125 mM glycine for 5 min at room temperature. Sonicated chromatin extract was immunoprecipitated overnight with corresponding antibodies. Protein A sepharose was used to capture immune complexes. Immune complexes were washed, de-crosslinked and DNA was extracted.
ChIP-seq libraries were prepared using the ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI)

value: MEF

value: mouse embryonic fibroblasts

value: USP44 Rescue

tag: chip antibody


title: CupR.rep1.Pos.Plate2.A6

value: 2 months


title: CupR.rep1.Pos.Plate2.A5

value: Remyelination


title: CupR.rep1.Pos.Plate2.A4


title: KO_USP44_H3K27Me3_Rep2


title: SVZ_Glast_D9_naive pJ [scNOME-seq]

value: IFN(A/G)R KO

value: naive


title: CupR.rep1.Pos.Plate2.A3


title: CupR.rep1.Pos.Plate2.A2


title: SVZ_Glast_D8_naive pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone

value: vSVZ astrocyte


title: CupR.rep1.Pos.Plate2.A12

value: Pos


title: CupR.rep1.Pos.Plate2.A11


title: KO_USP44_H3K27Me3_Rep1


title: SVZ_Glast_D18_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate2.A1


title: SVZ_Glast_D7_naive pJ [scNOME-seq]


title: KO_H3K27Me3_Rep1

value: USP44 KO


title: SVZ_Glast_D17_naive pJ [scNOME-seq]


title: KO_H3K27Me3_Rep3


title: CupR.rep1.Pos.Plate2.A10


title: CupR.rep1.Pos.Plate1.H9


title: WT Control 2


title: WT_H3K27Me3_Rep3


title: CupR.rep1.Pos.Plate1.H7


title: CupR.rep1.Pos.Plate1.H8


title: WT_H3K27Me3_Rep2


title: SVZ_Glast_D16_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.H5


title: SVZ_Glast_D15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.H2


title: CupR.rep1.Pos.Plate1.H6


title: CupR.rep1.Pos.Plate1.H3


title: WT_H3K27Me3_Rep1


title: CupR.rep1.Pos.Plate1.H4


title: SVZ_Glast_D14_naive pJ [scNOME-seq]


title: KO_H3K27Me3_Rep2


title: SVZ_Glast_D13_naive pJ [scNOME-seq]


title: KO_USP44_H3K27Ac_Rep3

value: H3K27Ac (Diagenode, C15410196)


title: CupR.rep1.Pos.Plate1.H10


title: SVZ_Glast_D12_naive pJ [scNOME-seq]

value: neuroblast


title: CupR.rep1.Pos.Plate1.H12


title: KO_USP44_H3K27Ac_Rep1


title: CupR.rep1.Pos.Plate1.G9


title: KO_USP44_H3K27Ac_Rep2


title: SVZ_Glast_D11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.G8


title: KO_H3K27Ac_Rep3


title: CupR.rep1.Pos.Plate1.G7


title: CupR.rep1.Pos.Plate1.H11


title: CupR.rep1.Pos.Plate1.G5


title: CupR.rep1.Pos.Plate1.G6


title: SVZ_Glast_C9_naive pJ [scNOME-seq]


title: KO_H3K27Ac_Rep2


title: SVZ_Glast_D10_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.G4


title: KO_H3K27Ac_Rep1


title: CupR.rep1.Pos.Plate1.G3


title: SVZ_Glast_C8_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.G2


title: CupR.rep1.Pos.Plate1.G12


title: CupR.rep1.Pos.Plate1.H1


title: WT_H3K27Ac_Rep3


title: WT_H3K27Ac_Rep2


title: CupR.rep1.Pos.Plate1.G1


title: SVZ_Glast_C7_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.F9


title: CupR.rep1.Pos.Plate1.G11


title: CupR.rep1.Pos.Plate1.G10


title: WT_H3K27Ac_Rep1


title: SVZ_Glast_C18_naive pJ [scNOME-seq]

value: TAP


title: KO_USP44_H3K4Me3_Rep3

value: H3K4Me3 (Diagenode, C15410003)


title: SVZ_Glast_C17_naive pJ [scNOME-seq]


title: SVZ_Glast_C16_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.F6

value: Corpus Callosum and Striatum


title: KO_USP44_H3K4Me3_Rep2


title: CupR.rep1.Pos.Plate1.F8

value: Isolated Microglia


title: CupR.rep1.Pos.Plate1.F5


title: CupR.rep1.Pos.Plate1.F4


title: KO_USP44_H3K4Me3_Rep1

value: MEF


title: SVZ_Glast_C15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.F3


title: SVZ_Glast_C14_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.F2


title: KO_H3K4Me3_Rep3

value: mouse embryonic fibroblasts


title: CupR.rep1.Pos.Plate1.F12


title: CupR.rep1.Pos.Plate1.F1


title: SVZ_Glast_C13_naive pJ [scNOME-seq]


title: KO_H3K4Me3_Rep2


title: SVZ_Glast_C12_naive pJ [scNOME-seq]


title: KO_H3K4Me3_Rep1


title: SVZ_Glast_C11_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.F11


title: CupR.rep1.Pos.Plate1.E8


title: CupR.rep1.Pos.Plate1.E7


title: CupR.rep1.Pos.Plate1.E9


title: CupR.rep1.Pos.Plate1.F7


title: SVZ_Glast_B9_naive pJ [scNOME-seq]


title: WT_H3K4Me3_Rep3

value: WT


title: WT_H3K4Me3_Rep2


title: SVZ_Glast_B8_naive pJ [scNOME-seq]


title: WT_H3K4Me3_Rep1


title: CupR.rep1.Pos.Plate1.E6

value: 2 months


title: CupR.rep1.Pos.Plate1.E4

value: Remyelination


title: CupR.rep1.Pos.Plate1.E5


title: CupR.rep1.Pos.Plate1.E3


title: SVZ_Glast_B7_naive pJ [scNOME-seq]

value: IFN(A/G)R KO


title: CupR.rep1.Pos.Plate1.E12


title: KO_USP44_UbH2B_Rep3

value: USP44 Rescue

value: Ubiquityl-Histone H2B (Lys120) (Cell Signaling, 5546)


title: CupR.rep1.Pos.Plate1.E2


title: CupR.rep1.Pos.Plate1.E11


title: CupR.rep1.Pos.Plate1.E10


title: KO_USP44_UbH2B_Rep2


title: SVZ_Glast_B18_naive pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone

value: vSVZ astrocyte

value: naive


title: CupR.rep1.Pos.Plate1.F10

value: Pos


title: SVZ_Glast_B17_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.E1


title: CupR.rep1.Pos.Plate1.D9


title: CupR.rep1.Pos.Plate1.D7


title: KO_UbH2B_Rep3

value: USP44 KO


title: CupR.rep1.Pos.Plate1.D8


title: CupR.rep1.Pos.Plate1.D6


title: SVZ_Glast_B16_naive pJ [scNOME-seq]

value: TAP


title: SVZ_Glast_B15_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.D5


title: CupR.rep1.Pos.Plate1.D4


title: KO_UbH2B_Rep2


title: CupR.rep1.Pos.Plate1.D3


title: SVZ_Glast_B14_naive pJ [scNOME-seq]


title: SVZ_Glast_B13_naive pJ [scNOME-seq]


title: WT_UbH2B_Rep3


title: CupR.rep1.Pos.Plate1.D11


title: CupR.rep1.Pos.Plate1.D2


title: SVZ_Glast_B12_naive pJ [scNOME-seq]


title: SVZ_Glast_B11_naive pJ [scNOME-seq]


title: WT_UbH2B_Rep2


title: WT_UbH2B_Rep1


title: CupR.rep1.Pos.Plate1.D12


title: KO_USP44_UbH2B_Rep1


title: CupR.rep1.Pos.Plate1.C9


title: CupR.rep1.Pos.Plate1.C8


title: CupR.rep1.Pos.Plate1.D10


title: KO_USP44_Input_Rep3

value: none (input)


title: CupR.rep1.Pos.Plate1.D1

value: Corpus Callosum and Striatum


title: CupR.rep1.Pos.Plate1.C7

value: Isolated Microglia


title: CupR.rep1.Pos.Plate1.C6


title: SVZ_Glast_A9_naive pJ [scNOME-seq]


title: KO_UbH2B_Rep1

value: MEF


title: CupR.rep1.Pos.Plate1.C5


title: CupR.rep1.Pos.Plate1.C4


title: KO_USP44_Input_Rep1

value: mouse embryonic fibroblasts


title: SVZ_Glast_A8_naive pJ [scNOME-seq]


title: KO_Input_Rep3


title: CupR.rep1.Pos.Plate1.C3


title: CupR.rep1.Pos.Plate1.C2


title: SVZ_Glast_A17_naive pJ [scNOME-seq]

value: neuroblast


title: SVZ_Glast_A7_naive pJ [scNOME-seq]


title: KO_Input_Rep2


title: CupR.rep1.Pos.Plate1.C10

value: 2 months


title: SVZ_Glast_A16_naive pJ [scNOME-seq]


title: SVZ_Glast_B10_naive pJ [scNOME-seq]


title: KO_Input_Rep1


title: CupR.rep1.Pos.Plate1.C1

value: Remyelination


title: CupR.rep1.Pos.Plate1.B8


title: SVZ_Glast_A15_naive pJ [scNOME-seq]

value: IFN(A/G)R KO


title: WT_Input_Rep3

value: WT


title: CupR.rep1.Pos.Plate1.B7


title: CupR.rep1.Pos.Plate1.B6


title: SVZ_Glast_A14_naive pJ [scNOME-seq]


title: KO_USP44_Input_Rep2

value: USP44 Rescue


title: CupR.rep1.Pos.Plate1.B4


title: CupR.rep1.Pos.Plate1.B5


title: SVZ_Glast_A13_naive pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: CupR.rep1.Pos.Plate1.B3


title: CupR.rep1.Pos.Plate1.B2


title: WT_Input_Rep1


title: CupR.rep1.Pos.Plate1.C12


title: KO_USP44_RNA_Rep3

data_processing:
All steps were performed with default settings unless otherwise denoted
Sequence reads were trimmed with fastx_trimmer (fastx/0.0.14)
Trimmed sequence reads were mapped to mm10 using star/2.7.9a
Read count extraction was performed using htseq/0.9.1 reverse strand option
Assembly: mm10
Supplementary files format and content: tab-deliminted text files include htseq-count values for each sample

extract_protocol:
Total RNA from MEF cells was isolated using QIAzol reagent and processed with RNeasy Plus Mini Kit (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina).


title: CupR.rep1.Pos.Plate1.C11


title: CupR.rep1.Pos.Plate1.B11


title: SVZ_Glast_A12_naive pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.B10


title: KO_USP44_RNA_Rep2


title: SVZ_Glast_A11_naive pJ [scNOME-seq]

value: vSVZ astrocyte


title: SVZ_Glast_A10_naive pJ [scNOME-seq]

value: naive


title: CupR.rep1.Pos.Plate1.B1

value: Pos


title: WT_Input_Rep2


title: CupR.rep1.Pos.Plate1.B9


title: CupR.rep1.Pos.Plate1.A9


title: KO_USP44_RNA_Rep1


title: CupR.rep1.Pos.Plate1.A8


title: KO_RNA_Rep3

value: USP44 KO


title: SVZ_Glast_P8_isch pJ [scNOME-seq]

value: aNSC

value: TiCY-IFN(A/G)R KO

value: 2 days post ischemia


title: CupR.rep1.Pos.Plate1.A6

value: Corpus Callosum and Striatum

value: Isolated Microglia


title: KO_RNA_Rep2

value: MEF

value: mouse embryonic fibroblasts


title: SVZ_Glast_P7_isch pJ [scNOME-seq]

value: neuroblast


title: SVZ_Glast_P6_isch pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.A5

value: Remyelination

value: 2 months


title: CupR.rep1.Pos.Plate1.B12


title: CupR.rep1.Pos.Plate1.A3


title: WT_RNA_Rep3

value: WT


title: SVZ_Glast_P5_isch pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.A12


title: SVZ_Glast_P3_isch pJ [scNOME-seq]


title: CupR.rep1.Pos.Plate1.A11


title: CupR.rep1.Pos.Plate1.A10


title: CupR.rep1.Pos.Plate1.A1


title: SVZ_Glast_P2_isch pJ [scNOME-seq]


title: WT_RNA_Rep1


title: CupR.rep1.Neg.Plate2.H9

value: Neg


title: CupR.rep1.Neg.Plate2.H8


title: CupR.rep1.Neg.Plate2.H7


title: CupR.rep1.Pos.Plate1.A7


title: MDA-MB-231, CFZ_combination_drug combination-treated, 8-hour treatment, rep1

city: Los Angeles

first: Yuanzhong

last: Pan

state: California

address: 1002 Childs Way

institute: University of Southern California

data_processing:
Raw reads in fastq format was processed with Trimmomatic to trim adaptor sequences, only paired reads were retained for downstream analysis
Quality control (QC) of trimmed and paried reads were done using fastqc
Paired reads that passed QC were mapped to hg38 assembly using hisat2
Mapped reads in bam format were processed using featureCounts to count number of reads for each gene
Assembly: hg38
Supplementary files format and content: tab-deliminated txt files containing raw counts for each samples

organism: Homo sapiens

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 media supplemented with 10% Fetal Bovine Serum (FBS) in humidified atmosphere at 37 degree celcius

extract_protocol:
Total RNA was extracted using NEB Monarch RNA miniprep kit following manufacturuer's protocol with on-column DNA digestion
Poly-A selection and library preparation was performed at Azenta according to their standard RNA-seq service package

treatment_protocol: Stock small molecules were dissolved in DMSO at a concentration of 10 mM and further diluted to 1000X of indicated using DMSO right before use. 1/1000 volume of drugs (or pure DMSO for control group) was added to fresh culture media, mixed thoroughly, and added to cultured cells.

value: Breast Cancer Cells

value: SHP1705 (10 µM) + Carfilzomib (10 nM)

tag: time


title: MDA-MB-231, CFZ_combination_CFZ-treated, 8-hour treatment, rep3

value: Carfilzomib (10 nM)


title: KO_RNA_Rep1


title: CupR.rep1.Neg.Plate2.H4


title: CupR.rep1.Pos.Plate1.A4

value: Pos


title: SVZ_Glast_P17_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone

value: vSVZ astrocyte


title: SVZ_Glast_P1_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO


title: SVZ_Glast_P18_isch pJ [scNOME-seq]

value: 2 days post ischemia


title: MDA-MB-231, CFZ_combination_CFZ-treated, 8-hour treatment, rep2


title: CupR.rep1.Pos.Plate1.A2

value: Corpus Callosum and Striatum


title: SVZ_Glast_P16_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.H3

value: Isolated Microglia


title: CupR.rep1.Neg.Plate2.H2


title: WT_RNA_Rep2

value: MEF


title: CupR.rep1.Neg.Plate2.H12


title: SVZ_Glast_P15_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 8-hour treatment, rep3


title: SVZ_Glast_P14_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.H10


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate2.H6


title: CupR.rep1.Neg.Plate2.H11


title: CupR.rep1.Neg.Plate2.G9


title: CupR.rep1.Neg.Plate2.H5


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 8-hour treatment, rep1


title: SVZ_Glast_P12_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.G7


title: CupR.rep1.Neg.Plate2.G8


title: MDA-MB-231, CFZ_combination_DMSO-treated, 8-hour treatment, rep3

value: DMSO


title: CupR.rep1.Neg.Plate2.G6


title: CupR.rep1.Neg.Plate2.G5


title: SVZ_Glast_P11_isch pJ [scNOME-seq]

value: neuroblast


title: MDA-MB-231, CFZ_combination_DMSO-treated, 8-hour treatment, rep2


title: MDA-MB-231, CFZ_combination_DMSO-treated, 8-hour treatment, rep1


title: MDA-MB-231, CFZ_combination_CFZ-treated, 8-hour treatment, rep1


title: SVZ_Glast_P10_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.G2

value: Remyelination


title: CupR.rep1.Neg.Plate2.G12

value: 2 months


title: SVZ_Glast_O8_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.G11


title: MDA-MB-231, MG_combination_drug combination-treated, 8-hour treatment, rep3


title: CupR.rep1.Neg.Plate2.G10


title: CupR.rep1.Neg.Plate2.G1


title: SVZ_Glast_O7_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.H1


title: SVZ_Glast_P13_isch pJ [scNOME-seq]


title: MDA-MB-231, MG_combination_drug combination-treated, 8-hour treatment, rep1


title: CupR.rep1.Neg.Plate2.F8


title: SVZ_Glast_O6_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.G4


title: MDA-MB-231, MG_combination_drug combination-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate2.F7


title: CupR.rep1.Neg.Plate2.F5


title: MDA-MB-231, MG_combination_MG132-treated, 8-hour treatment, rep3


title: CupR.rep1.Neg.Plate2.F6


title: CupR.rep1.Neg.Plate2.F4


title: SVZ_Glast_O4_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.G3


title: MDA-MB-231, MG_combination_MG132-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate2.F2


title: MDA-MB-231, MG_combination_MG132-treated, 8-hour treatment, rep1


title: CupR.rep1.Neg.Plate2.F3


title: CupR.rep1.Neg.Plate2.F11


title: SVZ_Glast_O18_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.F10


title: SVZ_Glast_O17_isch pJ [scNOME-seq]


title: MDA-MB-231, MG_combination_SHP1705-treated, 8-hour treatment, rep3


title: CupR.rep1.Neg.Plate2.E9


title: MDA-MB-231, MG_combination_SHP1705-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate2.F9


title: SVZ_Glast_O16_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.E7


title: SVZ_Glast_O15_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.E6


title: MDA-MB-231, MG_combination_SHP1705-treated, 8-hour treatment, rep1


title: CupR.rep1.Neg.Plate2.E5


title: SVZ_Glast_O14_isch pJ [scNOME-seq]


title: MDA-MB-231, MG_combination_DMSO-treated, 8-hour treatment, rep3


title: MDA-MB-231, MG_combination_DMSO-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate2.E3


title: SVZ_Glast_O1_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.F12


title: CupR.rep1.Neg.Plate2.E4


title: CupR.rep1.Neg.Plate2.E12


title: CupR.rep1.Neg.Plate2.E2


title: SVZ_Glast_O11_isch pJ [scNOME-seq]


title: SVZ_Glast_O12_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.E11


title: CupR.rep1.Neg.Plate2.E10


title: CupR.rep1.Neg.Plate2.F1


title: SVZ_Glast_O10_isch pJ [scNOME-seq]

value: aNSC


title: RPE1_sorted, HTO-derived cDNA

city: Cambridge

first: Adelyne

middle: SL

last: Chan

address: Li Ka Shing Way

department: Cancer Research UK

country: United Kingdom

institute: University of Cambridge

description: hashtag

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: tsv and matrix files

growth_protocol: RPE1-hTert cells were grown in DMEM/F12 with no phenol red, and passaged a minimum of twice per week or according to experiment design requirements. Cells were passaged on the day of 4OHT induction and on the day prior to harvest.

extract_protocol:
On the day of harvest, cells were trypsinised into suspension, labelled with the indicated hashtag antibodies and then pooled for single-cell encapsulation with the 10x Genomics platform.
Libraries were prepared according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics), the multiplexed cell suspension was loaded onto 2 lanes n the 10x Chromium Genomics platform for single cell encapsulation and library preparation according to the manufacturer’s instructions (10x Genomics Chromium Single Cell 3' GEM v3 workflow). Standard 10x Genomics parameters were used for sequencing: read1: 28bp, index1: 8bp, index2: 0bp, read2: 91bp. The libraries were sequenced on 1 lane of an S1 flowcell on an Illumina NovaSeq 6000.

treatment_protocol: Induced samples were treated with 100uM of 4OHT for the indicated time period.


title: CupR.rep1.Neg.Plate2.E1

value: Neg


title: RPE1_sorted, mRNA-derived cDNA


title: CupR.rep1.Neg.Plate2.D9


title: SVZ_Glast_N9_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.D8


title: XL_d6_rep5

data_processing:
Reads were quality checked with FastQC (Babraham Institute), aligned with STAR (Dobin et al. 2013) against the hg38 human genome build.
Uniquely mapping reads were summarised into counts using featureCounts from subread (Liao, Smyth and Shi 2013).
Differential expression analysis between conditions was performed using edgeR (Robinson, McCarthy nd Smyth 2010).
Assembly: hg38
Supplementary files format and content: Tab-separated values file

extract_protocol:
RNA was extracted using Qiagen Rneasy Plus using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: construct

tag: subpopulation

value: flow sorted – XL

value: 6 days 4OHT


title: CupR.rep1.Neg.Plate2.D7


title: SVZ_Glast_N8_isch pJ [scNOME-seq]

value: TAP


title: CupR.rep1.Neg.Plate2.D6


title: XL_d6_rep4


title: MDA-MB-231, MG_combination_DMSO-treated, 8-hour treatment, rep1

value: Breast Cancer Cells


title: CupR.rep1.Neg.Plate2.D5


title: XL_d6_rep3


title: SVZ_Glast_N7_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: CupR.rep1.Neg.Plate2.D4


title: CupR.rep1.Neg.Plate2.D3


title: CupR.rep1.Neg.Plate2.D2


title: SVZ_Glast_N6_isch pJ [scNOME-seq]


title: XL_d6_rep2


title: SVZ_Glast_N5_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.D11


title: SVZ_Glast_N4_isch pJ [scNOME-seq]


title: XL_d6_rep1


title: CupR.rep1.Neg.Plate2.D1


title: CupR.rep1.Neg.Plate2.D10


title: CupR.rep1.Neg.Plate2.C8


title: XL_d0_rep5

value: No Treat


title: CupR.rep1.Neg.Plate2.C7


title: CupR.rep1.Neg.Plate2.C6


title: CupR.rep1.Neg.Plate2.C9


title: SVZ_Glast_N3_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO


title: SVZ_Glast_N2_isch pJ [scNOME-seq]

value: 2 days post ischemia


title: CupR.rep1.Neg.Plate2.C5

value: Corpus Callosum and Striatum


title: XL_d0_rep3


title: CupR.rep1.Neg.Plate2.C4

value: Isolated Microglia


title: SVZ_Glast_N1_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.C2


title: CupR.rep1.Neg.Plate2.D12


title: XL_d0_rep2


title: SVZ_Glast_N18_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.C12


title: SVZ_Glast_N17_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.C3


title: S_d6_rep5

value: flow sorted – S


title: CupR.rep1.Neg.Plate2.C1


title: CupR.rep1.Neg.Plate2.C10


title: CupR.rep1.Neg.Plate2.C11


title: XL_d0_rep1


title: SVZ_Glast_N16_isch pJ [scNOME-seq]


title: XL_d0_rep4


title: S_d6_rep4


title: CupR.rep1.Neg.Plate2.B8


title: CupR.rep1.Neg.Plate2.B9


title: SVZ_Glast_N15_isch pJ [scNOME-seq]

value: vSVZ astrocyte


title: S_d6_rep3


title: SVZ_Glast_N14_isch pJ [scNOME-seq]

value: neuroblast


title: CupR.rep1.Neg.Plate2.B6

value: Remyelination


title: CupR.rep1.Neg.Plate2.B5

value: 2 months


title: S_d6_rep2


title: SVZ_Glast_N13_isch pJ [scNOME-seq]


title: S_d6_rep1


title: CupR.rep1.Neg.Plate2.B3


title: CupR.rep1.Neg.Plate2.B4


title: SVZ_Glast_N12_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.B2


title: S_d0_rep5


title: CupR.rep1.Neg.Plate2.B12


title: CupR.rep1.Neg.Plate2.B11


title: S_d0_rep4


title: CupR.rep1.Neg.Plate2.B10


title: SVZ_Glast_N11_isch pJ [scNOME-seq]

value: aNSC


title: CupR.rep1.Neg.Plate2.B1

value: Neg


title: SVZ_Glast_M9_isch pJ [scNOME-seq]


title: SVZ_Glast_M8_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.A9


title: CupR.rep1.Neg.Plate2.B7


title: S_d0_rep2


title: S_d0_rep3


title: CupR.rep1.Neg.Plate2.A8


title: CupR.rep1.Neg.Plate2.A7


title: S_d0_rep1


title: CupR.rep1.Neg.Plate2.A6


title: CupR.rep1.Neg.Plate2.A5


title: SVZ_Glast_M7_isch pJ [scNOME-seq]


title: SVZ_Glast_M6_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate2.E8


title: N_d6_rep5

value: parental control – N


title: CupR.rep1.Neg.Plate2.A4


title: CupR.rep1.Neg.Plate2.A3


title: CupR.rep1.Neg.Plate2.A2


title: CupR.rep1.Neg.Plate2.A12


title: N_d6_rep4

value: 6 days 4OHT


title: CupR.rep1.Neg.Plate2.A11


title: SVZ_Glast_M4_isch pJ [scNOME-seq]


title: N_d6_rep3


title: CupR.rep1.Neg.Plate2.A10


title: SVZ_Glast_M3_isch pJ [scNOME-seq]


title: N_d6_rep2


title: CupR.rep1.Neg.Plate2.A1


title: CupR.rep1.Neg.Plate1.H9


title: SVZ_Glast_M1_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.H8


title: N_d6_rep1


title: CupR.rep1.Neg.Plate1.H7


title: SVZ_Glast_M18_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.H5


title: CupR.rep1.Neg.Plate1.H6


title: N_d0_rep5


title: SVZ_Glast_M5_isch pJ [scNOME-seq]


title: N_d0_rep4


title: CupR.rep1.Neg.Plate1.H3


title: CupR.rep1.Neg.Plate1.H4


title: SVZ_Glast_M17_isch pJ [scNOME-seq]


title: SVZ_Glast_M15_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.H2


title: N_d0_rep3


title: CupR.rep1.Neg.Plate1.H12


title: SVZ_Glast_M14_isch pJ [scNOME-seq]


title: N_d0_rep2


title: CupR.rep1.Neg.Plate1.H10


title: SVZ_Glast_O5_isch pJ [scNOME-seq]


title: SVZ_Glast_M13_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.H1


title: N_d0_rep1


title: M_d6_rep4

value: flow sorted – M


title: M_d6_rep5


title: SVZ_Glast_M10_isch pJ [scNOME-seq]

value: TAP


title: CupR.rep1.Neg.Plate1.G6


title: CupR.rep1.Neg.Plate1.G9


title: SVZ_Glast_L8_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_L9_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.G4


title: CupR.rep1.Neg.Plate1.G7


title: CupR.rep1.Neg.Plate1.G3


title: M_d6_rep2


title: CupR.rep1.Neg.Plate1.G5


title: SVZ_Glast_L7_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.G2


title: CupR.rep1.Neg.Plate1.H11


title: M_d6_rep3


title: CupR.rep1.Neg.Plate1.G11


title: SVZ_Glast_L4_isch pJ [scNOME-seq]


title: M_d6_rep1


title: SVZ_Glast_L5_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.G12


title: CupR.rep1.Neg.Plate1.G1


title: CupR.rep1.Neg.Plate1.F9


title: M_d0_rep5

value: No Treat


title: CupR.rep1.Neg.Plate1.G8


title: CupR.rep1.Neg.Plate1.F8


title: M_d0_rep4


title: CupR.rep1.Neg.Plate1.F7


title: SVZ_Glast_L1_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO


title: CupR.rep1.Neg.Plate1.F6


title: M_d0_rep3


title: SVZ_Glast_L18_isch pJ [scNOME-seq]

value: 2 days post ischemia


title: CupR.rep1.Neg.Plate1.F5

value: Corpus Callosum and Striatum


title: SVZ_Glast_L17_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.G10

value: Isolated Microglia


title: CupR.rep1.Neg.Plate1.F3


title: M_d0_rep2


title: SVZ_Glast_L16_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.F2


title: CupR.rep1.Neg.Plate1.F4


title: M_d0_rep1


title: SVZ_Glast_L15_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.F12


title: CupR.rep1.Neg.Plate1.F11


title: L_d6_rep5

value: flow sorted – L


title: CupR.rep1.Neg.Plate1.F10


title: L_d6_rep4


title: CupR.rep1.Neg.Plate1.E9


title: CupR.rep1.Neg.Plate1.F1


title: CupR.rep1.Neg.Plate1.E8


title: SVZ_Glast_L13_isch pJ [scNOME-seq]


title: SVZ_Glast_L11_isch pJ [scNOME-seq]


title: L_d6_rep2


title: L_d6_rep1


title: SVZ_Glast_L10_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.E6


title: CupR.rep1.Neg.Plate1.E4


title: CupR.rep1.Neg.Plate1.E2


title: SVZ_Glast_K9_isch pJ [scNOME-seq]


title: L_d0_rep5


title: L_d0_rep4


title: SVZ_Glast_K8_isch pJ [scNOME-seq]

value: vSVZ astrocyte


title: CupR.rep1.Neg.Plate1.E10


title: CupR.rep1.Neg.Plate1.E11


title: CupR.rep1.Neg.Plate1.E1


title: SVZ_Glast_K6_isch pJ [scNOME-seq]


title: SVZ_Glast_L14_isch pJ [scNOME-seq]

value: neuroblast


title: CupR.rep1.Neg.Plate1.D9

value: Remyelination


title: CupR.rep1.Neg.Plate1.E7

value: 2 months


title: L_d6_rep3


title: L_d0_rep3


title: SVZ_Glast_K5_isch pJ [scNOME-seq]

value: aNSC


title: L_d0_rep1


title: CupR.rep1.Neg.Plate1.D6

value: Neg


title: CupR.rep1.Neg.Plate1.D8


title: SVZ_Glast_K4_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.D5


title: CupR.rep1.Neg.Plate1.D7


title: L_d0_rep2


title: CupR.rep1.Neg.Plate1.E5


title: CupR.rep1.Neg.Plate1.E3


title: SVZ_Glast_K3_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.E12


title: STARR-seq, MG_combination_drug combination-treated, 8-hour treatment

data_processing:
Raw reads in fastq format was processed with Trimmomatic to trim adaptor sequences, only paired reads were retained for downstream analysis
Quality control (QC) of trimmed and paried reads were done using fastqc
Paired reads that passed QC were mapped to hg38 assembly using bowtie2
Mapped reads in bam format were processed using MACS2 to call peaks
Assembly: hg38
Supplementary files format and content: peak files generated by the MACS2 peakcalling software
Library strategy: STARR-seq

extract_protocol:
Total RNA was extracted using QIAGEN RNA Maxiprep kit following manufacturuer's protocol.
Poly-A selection was done with Dynabeads. Reverse-transcription was done with SupreScript III. Library specific transcripts were expanded using junction PCR. Sequencing-ready library preparation was performed using PCR.

value: Breast Cancer Cells


title: CupR.rep1.Neg.Plate1.D4


title: STARR-seq, MG_combination_MG132-treated, 8-hour treatment


title: CupR.rep1.Neg.Plate1.D12


title: CupR.rep1.Neg.Plate1.D3


title: CupR.rep1.Neg.Plate1.D2


title: SVZ_Glast_K1_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.D10


title: SVZ_Glast_K18_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.D1


title: CupR.rep1.Neg.Plate1.C9


title: STARR-seq, MG_combination_DMSO-treated, 8-hour treatment

value: DMSO


title: SVZ_Glast_K17_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_drug combination-treated, 24-hour treatment, rep3

value: SHP1705 (10 µM) + Carfilzomib (10 nM)


title: CupR.rep1.Neg.Plate1.C7


title: CupR.rep1.Neg.Plate1.C8


title: CupR.rep1.Neg.Plate1.C5


title: MDA-MB-231, CFZ_combination_drug combination-treated, 24-hour treatment, rep2


title: SVZ_Glast_K15_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_drug combination-treated, 24-hour treatment, rep1


title: SVZ_Glast_K2_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.C3


title: SVZ_Glast_K14_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.C2


title: MDA-MB-231, CFZ_combination_CFZ-treated, 24-hour treatment, rep3

value: Carfilzomib (10 nM)


title: CupR.rep1.Neg.Plate1.C12


title: MDA-MB-231, CFZ_combination_CFZ-treated, 24-hour treatment, rep2


title: CupR.rep1.Neg.Plate1.C10


title: CupR.rep1.Neg.Plate1.D11


title: STARR-seq, MG_combination_SHP1705-treated, 8-hour treatment


title: SVZ_Glast_K12_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: CupR.rep1.Neg.Plate1.C1


title: CupR.rep1.Neg.Plate1.B9


title: MDA-MB-231, CFZ_combination_CFZ-treated, 24-hour treatment, rep1


title: SVZ_Glast_K11_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 24-hour treatment, rep3


title: SVZ_Glast_K16_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.C6


title: CupR.rep1.Neg.Plate1.B7


title: CupR.rep1.Neg.Plate1.B6


title: SVZ_Glast_K10_isch pJ [scNOME-seq]

value: TAP


title: CupR.rep1.Neg.Plate1.C4


title: CupR.rep1.Neg.Plate1.B5


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 24-hour treatment, rep2


title: SVZ_Glast_J9_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO


title: CupR.rep1.Neg.Plate1.B4


title: CupR.rep1.Neg.Plate1.B3


title: CupR.rep1.Neg.Plate1.C11


title: SVZ_Glast_K13_isch pJ [scNOME-seq]

value: 2 days post ischemia


title: MDA-MB-231, CFZ_combination_SHP1705-treated, 24-hour treatment, rep1


title: CupR.rep1.Neg.Plate1.B12

value: Corpus Callosum and Striatum


title: CupR.rep1.Neg.Plate1.B2

value: Isolated Microglia


title: SVZ_Glast_J7_isch pJ [scNOME-seq]


title: SVZ_Glast_J6_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_DMSO-treated, 24-hour treatment, rep3


title: CupR.rep1.Neg.Plate1.B11


title: CupR.rep1.Neg.Plate1.B10


title: SVZ_Glast_J5_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_DMSO-treated, 24-hour treatment, rep2


title: CupR.rep1.Neg.Plate1.B8


title: MDA-MB-231, CFZ_combination_DMSO-treated, 24-hour treatment, rep1


title: CupR.rep1.Neg.Plate1.A9


title: CupR.rep1.Neg.Plate1.B1


title: MDA-MB-231, CFZ_combination_drug combination-treated, 8-hour treatment, rep3


title: CupR.rep1.Neg.Plate1.A6


title: CupR.rep1.Neg.Plate1.A7


title: CupR.rep1.Neg.Plate1.A8


title: SVZ_Glast_J2_isch pJ [scNOME-seq]


title: MDA-MB-231, CFZ_combination_drug combination-treated, 8-hour treatment, rep2


title: CupR.rep1.Neg.Plate1.A5


title: SVZ_Glast_J1_isch pJ [scNOME-seq]


title: EKAB_Spinal Cord_6 wpi_rep2

first: Mayssa

middle: H

last: Mokalled

address: 4523 Clayton Ave, CB 8103

department: Developmental Biology

data_processing:
After sequencing, the Illumina output was processed using the CellRanger (v6.0.0) recommended pipeline to generate gene-barcode count matrices. A custom reference genome was made with the “cellranger mkref” command, using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build (https://useast.ensembl.org/Danio_rerio/Info/Index)  and the sorted Gene Transfer Format file (v4.3.2) from the improved zebrafish transcriptome annotation (Lawson et al., 2020)
Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then, the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene-barcode count matrices generated by “cellranger count” was used for downstream analysis.
All the datasets were integrated and analyzed using Seurat (v4.1.1) package with R (v4.2.1) (R Core Team, 2018; Stuart et al., 2019).  Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes, followed by cell quality assessment using commonly used QC matrixes (Ilicic et al., 2016). Cells having a unique number of genes between 200 to 4000 and a mitochondrial gene percentage <5 were used for downstream processing. Each dataset was independently normalized and scaled using the “SCTransform” function, which is an improved method for normalization, that performs a variance-stabilizing transformation using negative binomial regression (Hafemeister and Satija, 2019). Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors (Butler et al., 2018; Haghverdi et al., 2018).
Integration features were selected based on the top 4000 highly variable features using “SelectIntegrationFeatures” function (nfeatures = 4000), which was used as input for the “anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 4000 variable features and the top 50 principal components selected based on the elbow plot heuristic, which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph-based clustering on a shared nearest neighbor graph (Levine et al., 2015; Xu and Su, 2015). Louvain algorithm was used for modularity optimization in clustering the cells using “FindClusters” function. The resolution parameter (res = 0.5) that determines the granularity of the clustering was selected by visually inspecting clusters with resolutions ranging 0.1 - 2.0 as well as clustree graphs (Zappia and Oshlack, 2018). Uniform Manifold Approximation and Reduction (UMAP) was used for non-linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function (Becht et al., 2018). Data was graphed using different plot functions, such as “DimPlot”, “VlnPlot”, “FeaturePlot”, “Dotplot” and “DoHeatmap”, to view the cell cluster identity and marker gene expression. Cell proportion data was extracted using “table” and “prop.table” functions. Differential gene expression for individual cluster was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and with a logFC threshold of 0.25 were selected.
The clusters of interest were subclustered using the “subset” function for subcluster analysis. The subset was again normalized and scaled using “SCTransform” function with glmGamPoi method (Ahlmann-Eltze and Huber, 2021). Fifty principal components were used, and the resolution parameter was set to 0.5. Further downstream analysis was done as described above for the integrated analysis.
Assembly: GRCz11
Supplementary files format and content: Compressed tab separated files and matrix files

molecule: nuclear RNA

organism: Danio rerio

source_name: Spinal Cord

extract_protocol:
For snRNA-seq, 30 µl of resuspension solution containing isolated nuclei at a concentration of ~1000 nuclei/µl was submitted to sequencing.Two biological replicates of each timepoints at 0, 1, 3 and 6 wpi were used.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  cDNA was amplified for 11-13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.
The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

value: Spinal Cord

value: Wild type

value: Injured


title: CupR.rep1.Neg.Plate1.A3

value: Remyelination


title: SVZ_Glast_J18_isch pJ [scNOME-seq]

value: neuroblast


title: CupR.rep1.Neg.Plate1.A2

value: 2 months


title: CupR.rep1.Neg.Plate1.A12

value: Neg


title: EKAB_Spinal Cord_6 wpi_rep1

description: 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used


title: SVZ_Glast_J17_isch pJ [scNOME-seq]


title: CupR.rep1.Neg.Plate1.A11


title: CupR.rep1.Neg.Plate1.A10


title: CupR.rep1.Neg.Plate1.A1


title: SVZ_Glast_J4_isch pJ [scNOME-seq]

value: aNSC


title: SVZ_Glast_J16_isch pJ [scNOME-seq]


title: SVZ_Glast_J15_isch pJ [scNOME-seq]


title: EKAB_Spinal Cord_3 wpi_rep2


title: P7,Pos,KB0011,O23

source_name: Corpus Callosum and Cerebellum

value: Corpus Callosum and Cerebellum

value: Early Postnatal Homeostatic

value: Pos


title: SVZ_Glast_J14_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: P7,Pos,KB0011,E23

value: PAM


title: P7,Pos,KB0012,H23


title: EKAB_Spinal Cord_1 wpi_rep2


title: EKAB_Spinal Cord_1 wpi_rep1


title: EKAB_Spinal Cord_3 wpi_rep1


title: CupR.rep1.Neg.Plate1.A4


title: EKAB_Spinal Cord_Uninjured_rep2

value: Uninjured


title: P7,Pos,KB0011,M23


title: SVZ_Glast_J12_isch pJ [scNOME-seq]

value: TAP

value: TiCY-IFN(A/G)R KO

value: 2 days post ischemia


title: SVZ_Glast_J13_isch pJ [scNOME-seq]


title: P7,Pos,KB0011,A23

value: Isolated Microglia


title: SVZ_Glast_J11_isch pJ [scNOME-seq]

value: vSVZ astrocyte


title: P7,Pos,KB0011,K23


title: EKAB_Spinal Cord_Uninjured_rep1

value: Spinal Cord

value: Wild type


title: P7,Pos,KB0012,J23


title: SVZ_Glast_J10_isch pJ [scNOME-seq]


title: P7,Pos,KB0012,P23


title: S89-mDRIP-seq-Input-Col-0-cDNA

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
library strategy: mDRIP-seq
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
After trimming, clean reads were aligned to the genomes (BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice, TAIR10 genome for Arabidopsis, MSU version 7.0 for rice) with Bowtie 2 (version 2.2.5) using local alignment mode.
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice, TAIR10 genome for Arabidopsis, MSU version 7.0 for rice
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: Col-0 14d seedlings

extract_protocol:
For mammal and E. coli genomic DNA extraction, cells were lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For Arabidopsis and rice gDNA extraction, seedlings were grounded in liquid nitrogen and then lysed by 0.5% SDS and digested with 0.1 mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For yeast gDNA extraction, cells were resuspended in TE buffer with 0.5% NP40 and equal volume glass beads (Sigma#: G8772), and beat 6 times in 30 sec at 60 Hz with 1 min pausing at 4°C to destroy cell walls. Then cells were collected, lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For cDNA hybrids synthesis, total RNA was extracted according to the manual of TRIzol™ (ThermoFisher Scintific#:15596026) from the manufacturer. DNase I (ThermoFisher Scintific#: EN0521) treatment was performed at 37°C to remove potential gDNA contamination. cDNA hybrids were synthesized by ProtoScript® II Reverse Transcriptase with d(T)23VN primer according to the manufacturer’s manual. Then, cDNA hybrids were incubated with MBN at 30°C for 30 min to remove remaining primers and RNA while only production with DNA:RNA hybrid form can be retained.
Nucleic acid was digested with MBN at 30°C for 1 hour and purified using the phenol-chloroform nucleic acid extraction method followed by resuspending the pellet in 130 μl TE buffer. Sonication with Covaris™ ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4–20°C) was performed to fragment nucleic acid with peak size around 250 bp and quantified by Qubit™ dsDNA HS Assay Kit (ThermoFisher Scintific#:Q32851). For multiple samples that would be used as a pool for DRIP, sonicated DNA was diluted to the needed concentration and barcoded in DNA:RNA hybrids tailing and ligation reaction for each sample as above mentioned at 37°C for 1 hour with barcode adaptors (Table S2) followed by adding 2 μL 0.5 M EDTA to stop the reaction. Then, these barcoded samples were pooled together and purified using the phenol-chloroform nucleic acid extraction method. The purified nucleic acid pellet was resuspended in TE buffer followed by DRIP and library construction for sequencing as described in ssDRIP-seq.

value: Col-0 14d seedlings

value: WT

value: Untreated


title: S86-mDRIP-seq-Input-Col-0


title: P7,Neg,KB0015,O10

value: Neg


title: SVZ_Glast_I9_isch pJ [scNOME-seq]


title: P7,Neg,KB0015,K10

value: Corpus Callosum and Cerebellum

value: Divding


title: S85-mDRIP-seq-Input-Col-0


title: P7,Pos,KB0012,B23

value: Pos


title: P7,Pos,KB0012,D23


title: P7,Neg,KB0015,C1

value: Early Postnatal Homeostatic


title: SVZ_Glast_I8_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: P7,Neg,KB0015,I10


title: P7,Neg,KB0015,A1


title: SVZ_Glast_I6_isch pJ [scNOME-seq]

value: reactive astrocyte


title: P7,Neg,KB0015,M1


title: SVZ_Glast_I5_isch pJ [scNOME-seq]


title: P7,Neg,KB0015,G1


title: P7,Neg,KB0015,K1

value: Adult Brain Homeostatic


title: P7,Pos,KB0011,C23

value: PAM


title: S86-mDRIP-seq-Col-0


title: S85-mDRIP-seq-Col-0


title: SVZ_Glast_I4_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO

value: 2 days post ischemia


title: P7,Neg,KB0015,I1

value: Isolated Microglia


title: Normal Sample 3

city: Hualien

first: Mohammed Thangameeran

last: Shaik Ismail

state: Hualien

address: No. 701, Section 3, Zhongyang Rd

department: Institute of Medical Science

country: Taiwan

institute: Tzu Chi University

data_processing:
usegalaxy.eu; accession date: 14 February 2022
The RNA sequencing data analysis involved multiple steps for quality assurance and data processing. Initially, FastQC was used for quality assessment, and MultiQC compiled the results. Adapter sequences and low-quality bases were trimmed using Cutadapt, and the trimmed reads were reassessed for quality. The RNA STAR aligner was used for aligning reads against the rat reference genome (Rnor_6.0), with gene expression quantification done by featureCounts. Differential expression analysis was carried out using DESeq2, identifying differentially expressed genes with a fold change range from -3.012 to 7.539.
Assembly: The reference genome used for alignment was Rnor_6.0.
Supplementary files format and content: Tab-limited text files includes the normalized counts of each sample.
Supplementary files format and content: Tab-separated values file includes TPM values of each sample.

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat No. 250) according to the manufacturer's instructions.
Library preparation for RNA sequencing was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufactures protocol.

value: Striatum

tag: strain

value: Sprague-Dawley

tag: group

value: Normal


title: P7,Pos,KB0010,H11

value: DAM 1


title: P7,Pos,KB0011,G23


title: P7,Pos,KB0010,F11


title: SVZ_Glast_I1_isch pJ [scNOME-seq]

value: neuroblast


title: P7,Neg,KB0015,M10

value: Adult Spinal Cord Homeostatic

value: Neg


title: Normal Sample 2


title: P7,Pos,KB0010,N11

value: Corpus Callosum and Cerebellum


title: Normal Sample 1


title: SVZ_Glast_I18_isch pJ [scNOME-seq]


title: P7,Pos,KB0010,B11

value: Pos


title: S89-mDRIP-seq-Col-0-cDNA

value: Col-0 14d seedlings

value: WT

value: Untreated


title: Severe ICH Model Sample 4 (Day 1)

value: Injection of bacterial collagenase VII-S to induce ICH

value: Severe ICH Model


title: P7,Pos,KB0009,C11

value: PAM


title: P7,Pos,KB0009,G11

value: Early Postnatal Homeostatic


title: SVZ_Glast_I17_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone

value: TiCY-IFN(A/G)R KO

value: 2 days post ischemia


title: P7,Pos,KB0010,L11

value: Isolated Microglia


title: P7,Pos,KB0010,P11


title: Severe ICH Model Sample 3 (Day 1)

value: Striatum

value: Sprague-Dawley


title: P7,Pos,KB0010,J11


title: Severe ICH Model Sample 2 (Day 1)


title: P7,Neg,KB0015,C3


title: SVZ_Glast_I14_isch pJ [scNOME-seq]


title: P7,Neg,KB0015,O3


title: P7,Neg,KB0015,M3


title: SVZ_Glast_I12_isch pJ [scNOME-seq]


title: Severe ICH Model Sample 1 (Day 1)


title: P7,Neg,KB0015,E3


title: SVZ_Glast_I11_isch pJ [scNOME-seq]


title: P7,Neg,KB0015,K3


title: P7,Pos,KB0010,D11


title: ICH Model Sample 3 (Day 1)

value: ICH Model


title: P7,Neg,KB0015,G3

value: Neg


title: P7,Neg,KB0015,I3

value: Corpus Callosum and Cerebellum


title: SVZ_Glast_H9_isch pJ [scNOME-seq]

value: aNSC


title: SVZ_Glast_I15_isch pJ [scNOME-seq]

value: vSVZ astrocyte


title: P7,Pos,KB0010,N5

value: Adult Spinal Cord Homeostatic

value: Pos


title: ICH Model Sample  (Day 1)

value: Injection of bacterial collagenase VII-S to induce ICH


title: P7,Pos,KB0010,H5


title: P7,Pos,KB0010,D5


title: P7,Pos,KB0010,B5


title: ICH Model Sample 1 (Day 1)


title: SVZ_Glast_H8_isch pJ [scNOME-seq]

value: neuroblast


title: SVZ_Glast_H4_isch pJ [scNOME-seq]


title: SVZ_Glast_H7_isch pJ [scNOME-seq]


title: P7,Pos,KB0009,M5


title: P7,Pos,KB0010,J5


title: RCS_2KO_COL2_MUT_3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of RCS TFEB/3 DKO COL2R789C , biological rep3

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq; Trimming and cleaning with bbduk;Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: rn6
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Rat chondrosarcoma TFEB/3 DKO COL2R789C trasfected cells

growth_protocol: Cells were cultured in DMEM 10% FBS and 1% P/S at 37°C in 5% CO2.

extract_protocol:
Cells were harvested for RNA extraction using RNAeasy Mini Kit (Qiagen) accorging to manifacturer's instuctions. RNA extracted from MOCK cells was used as a control. RNA extracted was quantified and mixed at 50 ng/ul.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: Cells were reverse-transfected with mCHERRY-COL2R789C plasmid using Lipofectamine LTX and Plus reagent (Invitrogen) accorging to manifacturer's instuctions.

value: chondrocytes, bone derived cell line

tag: gender

value: unknown


title: SVZ_Glast_H3_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone


title: P7,Pos,KB0010,P5

value: Divding


title: RCS_2KO_COL2_MUT_1

description: Transcriptome profile of RCS TFEB/3 DKO COL2R789C , biological rep1


title: SVZ_Glast_H2_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO

value: 2 days post ischemia


title: RCS_2KO_COL2_MUT_2

description: Transcriptome profile of RCS TFEB/3 DKO COL2R789C , biological rep2


title: P7,Pos,KB0010,L5

value: Isolated Microglia


title: P7,Pos,KB0012,F17

value: PAM


title: ICH Model Sample 4 (Day 1)

value: Striatum

value: Sprague-Dawley

value: ICH Model


title: SVZ_Glast_H1_isch pJ [scNOME-seq]


title: P7,Pos,KB0011,E17

value: Corpus Callosum and Cerebellum

value: Early Postnatal Homeostatic


title: P7,Pos,KB0011,A17


title: RCS_COL2_MUT_3

description: Transcriptome profile of RCS COL2R789C , biological rep3

source_name: Rat chondrosarcoma WT COL2R789C trasfected cells


title: P7,Pos,KB0012,N17


title: SVZ_Glast_H18_isch pJ [scNOME-seq]


title: RCS_COL2_MUT_2

description: Transcriptome profile of RCS COL2R789C , biological rep2


title: P7,Pos,KB0011,M17


title: P7,Pos,KB0011,G17


title: SVZ_Glast_H16_isch pJ [scNOME-seq]


title: RCS_COL2_MUT_1

description: Transcriptome profile of RCS COL2R789C , biological rep1


title: SVZ_Glast_H15_isch pJ [scNOME-seq]

value: TAP


title: P7,Pos,KB0012,J17

value: Pos


title: P7,Pos,KB0012,L17


title: P7,Pos,KB0012,P17


title: SVZ_Glast_H14_isch pJ [scNOME-seq]


title: P7,Pos,KB0010,F3


title: P7,Pos,KB0010,H3

value: Adult Spinal Cord Homeostatic


title: P7,Pos,KB0012,H17


title: RCS_2KO_SCR_2

description: Transcriptome profile of RCS TFEB/3 DKO , biological rep2

source_name: Rat chondrosarcoma TFEB/3DKO cells scramble


title: SVZ_Glast_H13_isch pJ [scNOME-seq]

value: aNSC


title: P7,Pos,KB0009,E3


title: RCS_2KO_SCR_1

description: Transcriptome profile of RCS TFEB/3 DKO , biological rep1

value: chondrocytes, bone derived cell line


title: P7,Pos,KB0010,N3


title: SVZ_Glast_H12_isch pJ [scNOME-seq]


title: RCS_SCR_3

description: Transcriptome profile of RCS WT , biological rep3

source_name: Rat chondrosarcoma WT cells scramble

value: unknown


title: P7,Pos,KB0009,A3


title: P7,Pos,KB0010,D3


title: SVZ_Glast_H11_isch pJ [scNOME-seq]

value: striatum & ventricular-subventricular zone

value: neuroblast


title: RCS_SCR_2

description: Transcriptome profile of RCS WT , biological rep2


title: P7,Pos,KB0009,G3


title: SVZ_Glast_H10_isch pJ [scNOME-seq]

value: TiCY-IFN(A/G)R KO


title: P7,Pos,KB0010,L3


title: P7,Pos,KB0010,B3


title: P7,Pos,KB0009,I3

value: Divding


title: RCS_SCR_1

description: Transcriptome profile of RCS WT , biological rep1