title: SVZ_Glast_G16 pM

value: vSVZ astrocyte


title: FAD,rep2,Neg,Plate2,F11

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: Brain

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: Brain

tag: cell line

value: Isolated Microglia

tag: cell type

value: Adult Brain Homeostatic

tag: condition

tag: age

value: 4 months

tag: tdtom

value: Neg


title: SVZ_Glast_E9_naive pJ

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
single-cell RNA-seq
RNA_count_matrix.csv

library_source: transcriptomic single cell

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

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 transcriptomic portion of this multi-omic data set.

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

tag: genotype

value: IFN(A/G)R KO

tag: treatment

value: naive


title: SVZ_Glast_E8_naive pJ

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_G15 pM

value: TiCY


title: FAD,rep2,Neg,Plate2,F1

value: DAM 1


title: SVZ_Glast_F14_naive pJ


title: FAD,rep2,Neg,Plate2,E9


title: FAD,rep2,Neg,Plate2,G10


title: SVZ_Glast_E7_naive pJ

value: aNSC


title: FAD,rep2,Neg,Plate2,E8


title: SVZ_Glast_G14 pM

value: TAP


title: FAD,rep2,Neg,Plate2,E7

value: IEG+


title: SVZ_Glast_E18_naive pJ


title: FAD,rep2,Neg,Plate2,E6

value: Transitional DAM


title: SVZ_Glast_G13 pM


title: SVZ_Glast_G12 pM


title: FAD,rep2,Neg,Plate2,E5


title: SVZ_Glast_E17_naive pJ


title: FAD,rep2,Neg,Plate2,E4


title: SVZ_Glast_E16_naive pJ


title: SVZ_Glast_G11 pM

value: neuroblast


title: FAD,rep2,Neg,Plate2,E11


title: SVZ_Glast_E15_naive pJ


title: FAD,rep2,Neg,Plate2,D9


title: FAD,rep2,Neg,Plate2,E10


title: SVZ_Glast_G1 pM


title: SVZ_Glast_E14_naive pJ


title: FAD,rep2,Neg,Plate2,D8


title: SVZ_Glast_E13_naive pJ


title: SVZ_Glast_F9 pM


title: SVZ_Glast_G18 pM


title: FAD,rep2,Neg,Plate2,D7


title: SVZ_Glast_E12_naive pJ


title: FAD,rep2,Neg,Plate2,D5


title: SVZ_Glast_F8 pM


title: SVZ_Glast_E11_naive pJ


title: FAD,rep2,Neg,Plate2,D6


title: FAD,rep2,Neg,Plate2,D3


title: FAD,rep2,Neg,Plate2,D2


title: SVZ_Glast_F7 pM


title: FAD,rep2,Neg,Plate2,E3


title: FAD,rep2,Neg,Plate2,E2


title: SVZ_Glast_E10_naive pJ


title: FAD,rep2,Neg,Plate2,D10


title: SVZ_Glast_F6 pM


title: FAD,rep2,Neg,Plate2,D1


title: FAD,rep2,Neg,Plate2,D12


title: SVZ_Glast_G10 pM


title: FAD,rep2,Neg,Plate2,E1


title: FAD,rep2,Neg,Plate2,D11


title: SVZ_Glast_F5 pM


title: SVZ_Glast_D8_naive pJ


title: SVZ_Glast_F4 pM


title: FAD,rep2,Neg,Plate2,C8

value: Adult Spinal Cord Homeostatic


title: FAD,rep2,Neg,Plate2,C7


title: SVZ_Glast_D7_naive pJ


title: FAD,rep2,Neg,Plate2,C5


title: FAD,rep2,Neg,Plate2,C9


title: SVZ_Glast_F3 pM


title: FAD,rep2,Neg,Plate2,C4


title: SVZ_Glast_D18_naive pJ

value: vSVZ astrocyte


title: SVZ_Glast_F22 pM


title: FAD,rep2,Neg,Plate2,C10

value: Brain


title: SVZ_Glast_D17_naive pJ


title: SVZ_Glast_D9_naive pJ


title: FAD,rep2,Neg,Plate2,C11

value: Isolated Microglia


title: FAD,rep2,Neg,Plate2,B9


title: SVZ_Glast_F20 pM


title: SVZ_Glast_F21 pM


title: FAD,rep2,Neg,Plate2,C1


title: SVZ_Glast_D16_naive pJ


title: FAD,rep2,Neg,Plate2,B8

value: Adult Brain Homeostatic


title: SVZ_Glast_D15_naive pJ


title: SVZ_Glast_F19 pM


title: FAD,rep2,Neg,Plate2,B7

value: 4 months


title: SVZ_Glast_F18 pM


title: FAD,rep2,Neg,Plate2,B6

value: Neg


title: SVZ_Glast_D13_naive pJ

value: IFN(A/G)R KO


title: SVZ_Glast_D14_naive pJ

value: naive


title: FAD,rep2,Neg,Plate2,C6


title: FAD,rep2,Neg,Plate2,B12


title: SVZ_Glast_D12_naive pJ

value: striatum & ventricular-subventricular zone


title: FAD,rep2,Neg,Plate2,B10


title: FAD,rep2,Neg,Plate2,B11


title: SVZ_Glast_D11_naive pJ


title: SVZ_Glast_F16 pM

value: TiCY


title: FAD,rep2,Neg,Plate2,B1

value: DAM 1


title: SVZ_Glast_F15 pM

value: aNSC


title: SVZ_Glast_F14 pM


title: FAD,rep2,Neg,Plate2,A9


title: SVZ_Glast_D10_naive pJ


title: SVZ_Glast_G18_naive pJ


title: FAD,rep2,Neg,Plate2,A7


title: FAD,rep2,Neg,Plate2,A8


title: FAD,rep2,Neg,Plate2,B5


title: FAD,rep2,Neg,Plate2,A6


title: SVZ_Glast_F13 pM


title: FAD,rep2,Neg,Plate2,B4


title: SVZ_Glast_F17 pM


title: FAD,rep2,Neg,Plate2,B3


title: SVZ_Glast_C8_naive pJ


title: FAD,rep2,Neg,Plate2,A4


title: SVZ_Glast_F12 pM


title: FAD,rep2,Neg,Plate2,A2


title: FAD,rep2,Neg,Plate2,A3


title: SVZ_Glast_C7_naive pJ


title: SVZ_Glast_C18_naive pJ

value: TAP


title: SVZ_Glast_F11 pM


title: FAD,rep2,Neg,Plate2,A12


title: FAD,rep2,Neg,Plate2,A11


title: SVZ_Glast_C17_naive pJ


title: SVZ_Glast_F10 pM


title: FAD,rep2,Neg,Plate2,A1


title: FAD,rep2,Neg,Plate2,A10


title: FAD,rep2,Neg,Plate1,H9


title: SVZ_Glast_C16_naive pJ


title: SVZ_Glast_C9_naive pJ


title: FAD,rep2,Neg,Plate1,H7


title: SVZ_Glast_E9 pM


title: FAD,rep2,Neg,Plate2,A5

value: IEG+


title: FAD,rep2,Neg,Plate1,H8


title: FAD,rep2,Neg,Plate1,H6


title: FAD,rep2,Neg,Plate1,H3


title: SVZ_Glast_C15_naive pJ


title: SVZ_Glast_C13_naive pJ


title: SVZ_Glast_E8 pM


title: FAD,rep2,Neg,Plate1,H4

value: Transitional DAM


title: SVZ_Glast_C14_naive pJ


title: FAD,rep2,Neg,Plate1,H12


title: FAD,rep2,Neg,Plate1,H10


title: SVZ_Glast_E7 pM

value: neuroblast


title: FAD,rep2,Neg,Plate1,H11


title: SVZ_Glast_C12_naive pJ


title: SVZ_Glast_F1 pM


title: SVZ_Glast_C11_naive pJ


title: FAD,rep2,Neg,Plate1,H1


title: FAD,rep2,Neg,Plate1,G7


title: FAD,rep2,Neg,Plate1,G6


title: FAD,rep2,Neg,Plate1,G5


title: SVZ_Glast_B8_naive pJ


title: FAD,rep2,Neg,Plate1,H5


title: FAD,rep2,Neg,Plate1,G9


title: SVZ_Glast_E3 pM


title: SVZ_Glast_B9_naive pJ


title: SVZ_Glast_E22 pM


title: FAD,rep2,Neg,Plate1,G8


title: FAD,rep2,Neg,Plate1,G2


title: SVZ_Glast_B18_naive pJ


title: SVZ_Glast_E20 pM


title: SVZ_Glast_E5 pM


title: SVZ_Glast_E2 pM


title: SVZ_Glast_E21 pM


title: SVZ_Glast_B7_naive pJ


title: FAD,rep2,Neg,Plate1,H2


title: FAD,rep2,Neg,Plate1,G3


title: FAD,rep2,Neg,Plate1,G10


title: SVZ_Glast_E6 pM


title: FAD,rep2,Neg,Plate1,G11


title: FAD,rep2,Neg,Plate1,G12


title: SVZ_Glast_B15_naive pJ


title: SVZ_Glast_B17_naive pJ


title: SVZ_Glast_E19 pM


title: FAD,rep2,Neg,Plate1,G1


title: SVZ_Glast_E15 pM


title: SVZ_Glast_B13_naive pJ


title: SVZ_Glast_E14 pM


title: SVZ_Glast_B11_naive pJ


title: FAD,rep2,Neg,Plate1,F9


title: SVZ_Glast_B14_naive pJ


title: FAD,rep2,Neg,Plate1,F2


title: FAD,rep2,Neg,Plate1,G4


title: SVZ_Glast_E17 pM


title: FAD,rep2,Neg,Plate1,F10


title: SVZ_Glast_E18 pM


title: FAD,rep2,Neg,Plate1,F12


title: FAD,rep2,Neg,Plate1,F1


title: SVZ_Glast_E13 pM


title: SVZ_Glast_B10_naive pJ


title: FAD,rep2,Neg,Plate1,F8


title: FAD,rep2,Neg,Plate1,E9


title: FAD,rep2,Neg,Plate1,F7

value: Adult Spinal Cord Homeostatic


title: FAD,rep2,Neg,Plate1,F6


title: SVZ_Glast_E16 pM

value: vSVZ astrocyte


title: FAD,rep2,Neg,Plate1,F5

value: Brain


title: FAD,rep2,Neg,Plate1,F4

value: Isolated Microglia


title: SVZ_Glast_B12_naive pJ


title: FAD,rep2,Neg,Plate1,F3


title: SVZ_Glast_B16_naive pJ


title: FAD,rep2,Neg,Plate1,F11

value: Adult Brain Homeostatic


title: SVZ_Glast_A8_naive pJ


title: FAD,rep2,Neg,Plate1,E3

value: 4 months


title: SVZ_Glast_D9 pM


title: FAD,rep2,Neg,Plate1,E10

value: Neg


title: SVZ_Glast_D8 pM


title: FAD,rep2,Neg,Plate1,E11


title: FAD,rep2,Neg,Plate1,E8


title: SVZ_Glast_E12 pM


title: SVZ_Glast_E11 pM


title: SVZ_Glast_A15_naive pJ

value: IFN(A/G)R KO


title: FAD,rep2,Neg,Plate1,E7


title: FAD,rep2,Neg,Plate1,E4


title: FAD,rep2,Neg,Plate1,D8


title: SVZ_Glast_E10 pM

value: naive


title: SVZ_Glast_A14_naive pJ

value: striatum & ventricular-subventricular zone


title: FAD,rep2,Neg,Plate1,D5


title: SVZ_Glast_A7_naive pJ


title: FAD,rep2,Neg,Plate1,E2


title: FAD,rep2,Neg,Plate1,E12


title: FAD,rep2,Neg,Plate1,D4


title: FAD,rep2,Neg,Plate1,D3


title: SVZ_Glast_A17_naive pJ


title: FAD,rep2,Neg,Plate1,D12


title: FAD,rep2,Neg,Plate1,D11


title: SVZ_Glast_A16_naive pJ


title: SVZ_Glast_D22 pM

value: TiCY


title: FAD,rep2,Neg,Plate1,E1


title: SVZ_Glast_D7 pM


title: SVZ_Glast_A9_naive pJ


title: FAD,rep2,Neg,Plate1,D9


title: SVZ_Glast_D6 pM


title: SVZ_Glast_P7_isch pJ

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

value: 2 days post ischemia


title: FAD,rep2,Neg,Plate1,D7


title: FAD,rep2,Neg,Plate1,D6


title: SVZ_Glast_D2 pM


title: FAD,rep2,Neg,Plate1,C5


title: SVZ_Glast_A13_naive pJ


title: FAD,rep2,Neg,Plate1,C4


title: FAD,rep2,Neg,Plate1,D1


title: SVZ_Glast_D19 pM


title: SVZ_Glast_D4 pM


title: FAD,rep2,Neg,Plate1,C3


title: SVZ_Glast_A12_naive pJ


title: FAD,rep2,Neg,Plate1,D2


title: SVZ_Glast_D3 pM


title: SVZ_Glast_A11_naive pJ


title: FAD,rep2,Neg,Plate1,D10


title: FAD,rep2,Neg,Plate1,C12


title: SVZ_Glast_A10_naive pJ


title: SVZ_Glast_D21 pM


title: SVZ_Glast_D5 pM

value: TAP


title: SVZ_Glast_D15 pM


title: FAD,rep2,Neg,Plate1,C9

value: DAM 2


title: SVZ_Glast_P8_isch pJ

value: aNSC


title: SVZ_Glast_D20 pM


title: FAD,rep2,Neg,Plate1,C8


title: FAD,rep2,Neg,Plate1,B7


title: SVZ_Glast_P18_isch pJ

value: neuroblast


title: SVZ_Glast_D13 pM


title: SVZ_Glast_P3_isch pJ


title: FAD,rep2,Neg,Plate1,C7

value: DAM 1


title: FAD,rep2,Neg,Plate1,B5

value: Transitional DAM


title: FAD,rep2,Neg,Plate1,C6

value: Brain


title: FAD,rep2,Neg,Plate1,B4

value: Isolated Microglia


title: SVZ_Glast_D12 pM

value: vSVZ astrocyte


title: SVZ_Glast_P6_isch pJ


title: FAD,rep2,Neg,Plate1,B3

value: Adult Brain Homeostatic

value: 4 months


title: FAD,rep2,Neg,Plate1,C2

value: Neg


title: SVZ_Glast_D11 pM

value: naive


title: SVZ_Glast_D17 pM

value: striatum & ventricular-subventricular zone


title: FAD,rep2,Neg,Plate1,B11


title: SVZ_Glast_D10 pM

value: TiCY


title: SVZ_Glast_P17_isch pJ

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


title: FAD,rep2,Neg,Plate1,A9


title: FAD,rep2,Neg,Plate1,C11


title: FAD,rep2,Neg,Plate1,A8


title: SVZ_Glast_C9 pM


title: FAD,rep2,Neg,Plate1,A5


title: SVZ_Glast_D16 pM


title: FAD,rep2,Neg,Plate1,A4


title: FAD,rep2,Neg,Plate1,C10


title: FAD,rep2,Neg,Plate1,C1


title: FAD,rep2,Neg,Plate1,B9


title: SVZ_Glast_P2_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_P5_isch pJ


title: SVZ_Glast_P1_isch pJ


title: FAD,rep2,Neg,Plate1,B8

value: Adult Spinal Cord Homeostatic


title: FAD,rep2,Neg,Plate1,B6


title: SVZ_Glast_D14 pM


title: FAD,rep2,Neg,Plate1,A12


title: SVZ_Glast_C5 pM


title: SVZ_Glast_O8_isch pJ


title: FAD,rep1,Pos,Plate2,H9

value: DAM 2

value: Pos


title: SVZ_Glast_P16_isch pJ


title: FAD,rep2,Neg,Plate1,B2


title: SVZ_Glast_C4 pM


title: SVZ_Glast_P15_isch pJ


title: FAD,rep2,Neg,Plate1,B12


title: FAD,rep1,Pos,Plate2,H8


title: FAD,rep1,Pos,Plate2,H7


title: SVZ_Glast_P14_isch pJ

value: neuroblast


title: FAD,rep2,Neg,Plate1,B10


title: SVZ_Glast_O5_isch pJ


title: SVZ_Glast_D1 pM


title: FAD,rep2,Neg,Plate1,B1


title: SVZ_Glast_P13_isch pJ


title: SVZ_Glast_C22 pM


title: SVZ_Glast_P12_isch pJ


title: FAD,rep2,Neg,Plate1,A7


title: SVZ_Glast_C21 pM


title: FAD,rep2,Neg,Plate1,A6

value: DAM 1


title: SVZ_Glast_C8 pM


title: SVZ_Glast_P11_isch pJ


title: SVZ_Glast_C7 pM


title: FAD,rep1,Pos,Plate2,H12

value: MHCII+


title: FAD,rep2,Neg,Plate1,A3

value: Brain

value: Transitional DAM


title: FAD,rep1,Pos,Plate2,H1

value: Isolated Microglia


title: SVZ_Glast_C2 pM

value: vSVZ astrocyte


title: FAD,rep2,Neg,Plate1,A2

value: 4 months


title: FAD,rep2,Neg,Plate1,A10

value: Neg


title: FAD,rep2,Neg,Plate1,A1

value: Adult Brain Homeostatic


title: FAD,rep1,Pos,Plate2,G9


title: SVZ_Glast_O7_isch pJ

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_P10_isch pJ


title: FAD,rep1,Pos,Plate2,H2


title: FAD,rep1,Pos,Plate2,G8


title: FAD,rep1,Pos,Plate2,G7


title: SVZ_Glast_C6 pM

value: TiCY

value: naive


title: FAD,rep1,Pos,Plate2,G5


title: SVZ_Glast_O6_isch pJ

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

value: 2 days post ischemia


title: SVZ_Glast_C3 pM


title: FAD,rep1,Pos,Plate2,H6


title: FAD,rep1,Pos,Plate2,H5

value: DAM 2


title: SVZ_Glast_O4_isch pJ


title: FAD,rep1,Pos,Plate2,H3

value: Pos


title: SVZ_Glast_O1_isch pJ

value: neuroblast


title: SVZ_Glast_C17 pM


title: FAD,rep1,Pos,Plate2,H10

value: Adult Spinal Cord Homeostatic


title: FAD,rep1,Pos,Plate2,G2

value: DAM 1


title: FAD,rep1,Pos,Plate2,G12

value: Brain


title: FAD,rep1,Pos,Plate2,F9


title: SVZ_Glast_C20 pM


title: FAD,rep1,Pos,Plate2,F8


title: SVZ_Glast_O12_isch pJ


title: SVZ_Glast_O18_isch pJ


title: SVZ_Glast_O11_isch pJ


title: FAD,rep1,Pos,Plate2,H4


title: SVZ_Glast_O17_isch pJ


title: SVZ_Glast_O15_isch pJ


title: FAD,rep1,Pos,Plate2,F12


title: SVZ_Glast_C12 pM

value: TAP


title: SVZ_Glast_O16_isch pJ


title: FAD,rep1,Pos,Plate2,F10

value: Isolated Microglia


title: FAD,rep1,Pos,Plate2,F1

value: Transitional DAM


title: SVZ_Glast_C19 pM


title: FAD,rep1,Pos,Plate2,E8

value: 4 months


title: FAD,rep1,Pos,Plate2,F5


title: FAD,rep1,Pos,Plate2,G4


title: SVZ_Glast_C18 pM


title: FAD,rep1,Pos,Plate2,E7


title: SVZ_Glast_O14_isch pJ

value: vSVZ astrocyte


title: FAD,rep1,Pos,Plate2,G1


title: FAD,rep1,Pos,Plate2,E6


title: SVZ_Glast_C16 pM


title: SVZ_Glast_N4_isch pJ

value: aNSC


title: FAD,rep1,Pos,Plate2,E4


title: FAD,rep1,Pos,Plate2,E3


title: FAD,rep1,Pos,Plate2,E2


title: SVZ_Glast_C15 pM

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_N3_isch pJ


title: SVZ_Glast_N5_isch pJ


title: SVZ_Glast_C1 pM

value: TiCY


title: FAD,rep1,Pos,Plate2,F6


title: SVZ_Glast_B6 pM

value: naive


title: SVZ_Glast_C14 pM


title: SVZ_Glast_O10_isch pJ

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


title: SVZ_Glast_N2_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_B5 pM


title: FAD,rep1,Pos,Plate2,F4


title: FAD,rep1,Pos,Plate2,F3


title: SVZ_Glast_C13 pM


title: FAD,rep1,Pos,Plate2,F2


title: SVZ_Glast_N9_isch pJ


title: SVZ_Glast_C11 pM


title: SVZ_Glast_N8_isch pJ


title: SVZ_Glast_N18_isch pJ


title: FAD,rep1,Pos,Plate2,F11


title: FAD,rep1,Pos,Plate2,E9

value: DAM 2


title: SVZ_Glast_N7_isch pJ


title: SVZ_Glast_C10 pM


title: SVZ_Glast_N6_isch pJ


title: FAD,rep1,Pos,Plate2,D5

value: Pos


title: FAD,rep1,Pos,Plate2,D6


title: FAD,rep1,Pos,Plate2,D2


title: FAD,rep1,Pos,Plate2,E5


title: FAD,rep1,Pos,Plate2,D12


title: SVZ_Glast_B8 pM


title: FAD,rep1,Pos,Plate2,D11

value: PAM


title: SVZ_Glast_B7 pM


title: FAD,rep1,Pos,Plate2,D10


title: SVZ_Glast_B20 pM


title: FAD,rep1,Pos,Plate2,D1


title: SVZ_Glast_N14_isch pJ

value: neuroblast


title: FAD,rep1,Pos,Plate2,D8


title: FAD,rep1,Pos,Plate2,E11


title: FAD,rep1,Pos,Plate2,E10

value: Early Postnatal Homeostatic


title: SVZ_Glast_N1_isch pJ


title: FAD,rep1,Pos,Plate2,E1

value: Brain

value: DAM 1


title: SVZ_Glast_N15_isch pJ


title: SVZ_Glast_B4 pM


title: FAD,rep1,Pos,Plate2,D9

value: Isolated Microglia


title: FAD,rep1,Pos,Plate2,E12


title: SVZ_Glast_N11_isch pJ


title: FAD,rep1,Pos,Plate2,C5


title: FAD,rep1,Pos,Plate2,D7


title: SVZ_Glast_B3 pM


title: SVZ_Glast_B22 pM


title: SVZ_Glast_N17_isch pJ


title: FAD,rep1,Pos,Plate2,D4


title: FAD,rep1,Pos,Plate2,C2


title: SVZ_Glast_N16_isch pJ


title: SVZ_Glast_B18 pM


title: SVZ_Glast_M8_isch pJ


title: FAD,rep1,Pos,Plate2,C11


title: SVZ_Glast_B21 pM


title: SVZ_Glast_B14 pM


title: SVZ_Glast_B15 pM


title: SVZ_Glast_B13 pM


title: FAD,rep1,Pos,Plate2,B8

value: Divding


title: FAD,rep1,Pos,Plate2,C9

value: 4 months


title: FAD,rep1,Pos,Plate2,C3


title: SVZ_Glast_B2 pM

value: vSVZ astrocyte


title: SVZ_Glast_N13_isch pJ


title: FAD,rep1,Pos,Plate2,B7


title: FAD,rep1,Pos,Plate2,B6


title: FAD,rep1,Pos,Plate2,C8


title: SVZ_Glast_M5_isch pJ


title: SVZ_Glast_B10 pM


title: FAD,rep1,Pos,Plate2,B4


title: SVZ_Glast_N12_isch pJ


title: FAD,rep1,Pos,Plate2,C6


title: SVZ_Glast_B17 pM


title: FAD,rep1,Pos,Plate2,C4


title: FAD,rep1,Pos,Plate2,B12


title: SVZ_Glast_B16 pM


title: FAD,rep1,Pos,Plate2,B10


title: SVZ_Glast_M9_isch pJ

value: aNSC


title: FAD,rep1,Pos,Plate2,C7


title: FAD,rep1,Pos,Plate2,C12


title: FAD,rep1,Pos,Plate2,C10


title: SVZ_Glast_M7_isch pJ

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_B12 pM

value: TiCY


title: SVZ_Glast_M6_isch pJ


title: FAD,rep1,Pos,Plate2,B5


title: SVZ_Glast_A8 pM

value: naive


title: FAD,rep1,Pos,Plate2,A5


title: SVZ_Glast_M4_isch pJ

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


title: FAD,rep1,Pos,Plate2,C1

value: Transitional DAM


title: FAD,rep1,Pos,Plate2,B1


title: FAD,rep1,Pos,Plate2,B3


title: SVZ_Glast_B1 pM


title: FAD,rep1,Pos,Plate2,B2

value: Adult Brain Homeostatic


title: SVZ_Glast_M3_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_A9 pM


title: FAD,rep1,Pos,Plate2,B11

value: Pos


title: SVZ_Glast_M1_isch pJ


title: FAD,rep1,Pos,Plate2,A9

value: DAM 2


title: FAD,rep1,Pos,Plate2,A11

value: Adult Spinal Cord Homeostatic


title: SVZ_Glast_A3 pM


title: SVZ_Glast_A7 pM


title: SVZ_Glast_A22 pM


title: FAD,rep1,Pos,Plate1,H8

value: Brain


title: FAD,rep1,Pos,Plate2,A7

value: DAM 1


title: SVZ_Glast_M15_isch pJ

value: neuroblast


title: FAD,rep1,Pos,Plate2,A6

value: Isolated Microglia

value: PAM


title: FAD,rep1,Pos,Plate2,A8

value: 4 months


title: SVZ_Glast_M17_isch pJ


title: SVZ_Glast_L9_isch pJ


title: FAD,rep1,Pos,Plate1,H7


title: SVZ_Glast_M18_isch pJ


title: FAD,rep1,Pos,Plate2,A4


title: SVZ_Glast_A21 pM

value: vSVZ astrocyte


title: SVZ_Glast_M14_isch pJ

value: striatum & ventricular-subventricular zone


title: FAD,rep1,Pos,Plate2,A3

value: MHCII+


title: SVZ_Glast_L7_isch pJ


title: SVZ_Glast_M13_isch pJ


title: SVZ_Glast_A6 pM

value: TiCY

value: naive


title: SVZ_Glast_A4 pM


title: FAD,rep1,Pos,Plate2,A12


title: FAD,rep1,Pos,Plate1,G9


title: SVZ_Glast_M10_isch pJ

value: TAP

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


title: SVZ_Glast_A5 pM


title: FAD,rep1,Pos,Plate2,A10


title: FAD,rep1,Pos,Plate1,G7

value: Transitional DAM


title: FAD,rep1,Pos,Plate2,A1

value: Pos


title: SVZ_Glast_L4_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_A18 pM


title: FAD,rep1,Pos,Plate1,G2


title: FAD,rep1,Pos,Plate1,H6


title: FAD,rep1,Pos,Plate1,G11


title: SVZ_Glast_L1_isch pJ


title: SVZ_Glast_L8_isch pJ


title: FAD,rep1,Pos,Plate1,H3


title: SVZ_Glast_A20 pM


title: SVZ_Glast_L5_isch pJ


title: FAD,rep1,Pos,Plate1,G8


title: SVZ_Glast_A2 pM


title: FAD,rep1,Pos,Plate1,H10

value: Adult Spinal Cord Homeostatic


title: SVZ_Glast_A19 pM


title: FAD,rep1,Pos,Plate1,G6

value: Brain


title: FAD,rep1,Pos,Plate1,F9


title: SVZ_Glast_A16 pM


title: SVZ_Glast_L17_isch pJ


title: FAD,rep1,Pos,Plate1,G4


title: SVZ_Glast_A15 pM

value: aNSC


title: SVZ_Glast_A17 pM


title: FAD,rep1,Pos,Plate1,F4

value: DAM 1


title: FAD,rep1,Pos,Plate1,H12

value: Isolated Microglia


title: FAD,rep1,Pos,Plate1,F3


title: SVZ_Glast_L15_isch pJ

value: neuroblast


title: SVZ_Glast_L18_isch pJ


title: SVZ_Glast_A11 pM


title: SVZ_Glast_L11_isch pJ


title: FAD,rep1,Pos,Plate1,E9

value: 4 months


title: FAD,rep1,Pos,Plate1,E7


title: FAD,rep1,Pos,Plate1,F11


title: FAD,rep1,Pos,Plate1,E4


title: FAD,rep1,Pos,Plate1,F7


title: FAD,rep1,Pos,Plate1,E3


title: FAD,rep1,Pos,Plate1,F6


title: SVZ_Glast_A1 pM

value: vSVZ astrocyte


title: FAD,rep1,Pos,Plate1,E12


title: SVZ_Glast_L16_isch pJ

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_A14 pM


title: SVZ_Glast_A13 pM


title: FAD,rep1,Pos,Plate1,F10


title: FAD,rep1,Pos,Plate1,F12


title: SVZ_Glast_A12 pM


title: SVZ_Glast_L14_isch pJ


title: SVZ_Glast_L13_isch pJ


title: FAD,rep1,Pos,Plate1,E8


title: Str_Glast_P9 pM

value: astrocyte (striatum)


title: FAD,rep1,Pos,Plate1,E6

value: DAM 2


title: FAD,rep1,Pos,Plate1,E2


title: SVZ_Glast_A10 pM

value: TiCY

value: naive


title: SVZ_Glast_K6_isch pJ

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


title: FAD,rep1,Pos,Plate1,D7

value: IEG+


title: Str_Glast_P8 pM


title: SVZ_Glast_K9_isch pJ


title: FAD,rep1,Pos,Plate1,D6

value: Pos


title: Str_Glast_P4 pM


title: FAD,rep1,Pos,Plate1,E11


title: FAD,rep1,Pos,Plate1,D3

value: Transitional DAM


title: FAD,rep1,Pos,Plate1,E10


title: FAD,rep1,Pos,Plate1,D9


title: SVZ_Glast_K8_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_K3_isch pJ


title: Str_Glast_P23 pM


title: FAD,rep1,Pos,Plate1,C9

value: Brain


title: SVZ_Glast_K2_isch pJ


title: Str_Glast_P20 pM


title: FAD,rep1,Pos,Plate1,D4


title: FAD,rep1,Pos,Plate1,C7


title: FAD,rep1,Pos,Plate1,C4


title: SVZ_Glast_K1_isch pJ


title: FAD,rep1,Pos,Plate1,C12


title: SVZ_Glast_L10_isch pJ


title: FAD,rep1,Pos,Plate1,D8


title: FAD,rep1,Pos,Plate1,C10


title: Str_Glast_P7 pM


title: SVZ_Glast_K16_isch pJ


title: FAD,rep1,Pos,Plate1,C1


title: FAD,rep1,Pos,Plate1,B8


title: SVZ_Glast_K5_isch pJ

value: aNSC


title: SVZ_Glast_K15_isch pJ


title: FAD,rep1,Pos,Plate1,B7


title: SVZ_Glast_K4_isch pJ


title: FAD,rep1,Pos,Plate1,D12


title: FAD,rep1,Pos,Plate1,B6

value: DAM 1


title: SVZ_Glast_K14_isch pJ


title: Str_Glast_P21 pM


title: FAD,rep1,Pos,Plate1,D11

value: Isolated Microglia


title: FAD,rep1,Pos,Plate1,D10


title: SVZ_Glast_K13_isch pJ


title: FAD,rep1,Pos,Plate1,B2


title: SVZ_Glast_K12_isch pJ


title: FAD,rep1,Pos,Plate1,B10


title: Str_Glast_P1 pM


title: SVZ_Glast_K11_isch pJ


title: FAD,rep1,Pos,Plate1,C8

value: Adult Spinal Cord Homeostatic


title: Str_Glast_P2 pM


title: FAD,rep1,Pos,Plate1,A9

value: 4 months


title: FAD,rep1,Pos,Plate1,B1


title: SVZ_Glast_K17_isch pJ


title: SVZ_Glast_K18_isch pJ


title: Str_Glast_P18 pM


title: FAD,rep1,Pos,Plate1,C11


title: FAD,rep1,Pos,Plate1,C3


title: Str_Glast_P17 pM


title: FAD,rep1,Pos,Plate1,A8


title: Str_Glast_O9 pM


title: FAD,rep1,Pos,Plate1,B12


title: FAD,rep1,Pos,Plate1,A6


title: Str_Glast_P16 pM


title: Str_Glast_P14 pM


title: FAD,rep1,Pos,Plate1,B9


title: Str_Glast_P13 pM


title: Str_Glast_P11 pM


title: FAD,rep1,Pos,Plate1,B11


title: Str_Glast_O6 pM


title: FAD,rep1,Pos,Plate1,B4


title: FAD,rep1,Pos,Plate1,A10


title: SVZ_Glast_J6_isch pJ

value: neuroblast


title: SVZ_Glast_K10_isch pJ

value: striatum & ventricular-subventricular zone

value: TAP


title: FAD,rep1,Pos,Plate1,A1

value: DAM 2


title: FAD,rep1,Pos,Plate1,A4


title: Str_Glast_O8 pM

value: astrocyte (striatum)

value: TiCY


title: FAD,rep1,Neg,Plate2,H9

value: Adult Brain Homeostatic

value: Neg


title: Str_Glast_O5 pM

value: naive


title: FAD,rep1,Pos,Plate1,A2

value: Pos


title: SVZ_Glast_J7_isch pJ

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

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate2,H7

value: Brain


title: FAD,rep1,Neg,Plate2,H8

value: Transitional DAM


title: SVZ_Glast_J4_isch pJ

value: aNSC


title: SVZ_Glast_J5_isch pJ


title: Str_Glast_O3 pM


title: Str_Glast_O4 pM


title: SVZ_Glast_J2_isch pJ


title: Str_Glast_O7 pM


title: FAD,rep1,Neg,Plate2,H6

value: Isolated Microglia

value: DAM 1


title: FAD,rep1,Pos,Plate1,A11

value: 4 months


title: FAD,rep1,Neg,Plate2,H4


title: SVZ_Glast_J9_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_O22 pM


title: FAD,rep1,Pos,Plate1,A12


title: SVZ_Glast_J1_isch pJ

value: vSVZ astrocyte


title: FAD,rep1,Neg,Plate2,H11


title: Str_Glast_O20 pM


title: SVZ_Glast_J18_isch pJ

value: neuroblast


title: SVZ_Glast_J17_isch pJ

value: TAP


title: Str_Glast_O2 pM

value: astrocyte (striatum)

value: TiCY


title: FAD,rep1,Neg,Plate2,H10

value: Neg


title: FAD,rep1,Neg,Plate2,H5

value: Adult Brain Homeostatic


title: FAD,rep1,Neg,Plate2,G7

value: Adult Spinal Cord Homeostatic


title: FAD,rep1,Neg,Plate2,G9

value: IEG+


title: SVZ_Glast_J16_isch pJ

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

value: 2 days post ischemia


title: SVZ_Glast_J15_isch pJ


title: FAD,rep1,Neg,Plate2,G5

value: Brain


title: Str_Glast_O12 pM

value: naive


title: FAD,rep1,Neg,Plate2,G2

value: Isolated Microglia


title: Str_Glast_O13 pM


title: SVZ_Glast_J14_isch pJ


title: FAD,rep1,Neg,Plate2,G3


title: Str_Glast_O17 pM


title: FAD,rep1,Neg,Plate2,G12


title: FAD,rep1,Neg,Plate2,H3

value: Transitional DAM


title: FAD,rep1,Neg,Plate2,H12

value: 4 months


title: FAD,rep1,Neg,Plate2,G6


title: FAD,rep1,Neg,Plate2,G11


title: SVZ_Glast_J12_isch pJ

value: striatum & ventricular-subventricular zone


title: FAD,rep1,Neg,Plate2,G4


title: FAD,rep1,Neg,Plate2,H1


title: FAD,rep1,Neg,Plate2,G10


title: Str_Glast_O18 pM


title: FAD,rep1,Neg,Plate2,G8


title: FAD,rep1,Neg,Plate2,G1


title: Str_Glast_O10 pM


title: SVZ_Glast_J11_isch pJ

value: vSVZ astrocyte


title: Str_Glast_O11 pM


title: FAD,rep1,Neg,Plate2,F8


title: Str_Glast_O1 pM


title: FAD,rep1,Neg,Plate2,F9


title: Str_Glast_N9 pM


title: SVZ_Glast_J10_isch pJ


title: FAD,rep1,Neg,Plate2,F4

value: DAM 2


title: FAD,rep1,Neg,Plate2,F5


title: Str_Glast_N8 pM


title: FAD,rep1,Neg,Plate2,F3


title: SVZ_Glast_I9_isch pJ


title: FAD,rep1,Neg,Plate2,F2


title: Str_Glast_N7 pM


title: FAD,rep1,Neg,Plate2,F7


title: FAD,rep1,Neg,Plate2,F6


title: FAD,rep1,Neg,Plate2,F12


title: Str_Glast_N6 pM


title: SVZ_Glast_I6_isch pJ

value: reactive astrocyte


title: SVZ_Glast_I5_isch pJ


title: FAD,rep1,Neg,Plate2,F11


title: FAD,rep1,Neg,Plate2,F1


title: SVZ_Glast_I4_isch pJ


title: Str_Glast_N4 pM

value: astrocyte (striatum)


title: FAD,rep1,Neg,Plate2,F10

value: Early Postnatal Homeostatic


title: FAD,rep1,Neg,Plate2,E9

value: Neg


title: FAD,rep1,Neg,Plate2,E8


title: SVZ_Glast_I8_isch pJ


title: Str_Glast_N5 pM

value: TiCY


title: FAD,rep1,Neg,Plate2,E6


title: FAD,rep1,Neg,Plate2,E7


title: SVZ_Glast_I18_isch pJ


title: SVZ_Glast_I1_isch pJ

value: neuroblast


title: Str_Glast_N3 pM


title: SVZ_Glast_J13_isch pJ


title: Str_Glast_N23 pM


title: FAD,rep1,Neg,Plate2,E4

value: IEG+


title: FAD,rep1,Neg,Plate2,E12


title: SVZ_Glast_I15_isch pJ

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


title: Str_Glast_N24 pM


title: SVZ_Glast_I14_isch pJ

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate2,E1

value: Brain


title: FAD,rep1,Neg,Plate2,E10

value: Adult Spinal Cord Homeostatic


title: SVZ_Glast_I17_isch pJ


title: FAD,rep1,Neg,Plate2,E2

value: Isolated Microglia


title: FAD,rep1,Neg,Plate2,D9


title: Str_Glast_N22 pM

value: naive


title: FAD,rep1,Neg,Plate2,E5

value: 4 months


title: Str_Glast_N20 pM

value: striatum & ventricular-subventricular zone


title: FAD,rep1,Neg,Plate2,E3


title: SVZ_Glast_I12_isch pJ


title: SVZ_Glast_I11_isch pJ


title: Str_Glast_N19 pM


title: FAD,rep1,Neg,Plate2,D6


title: SVZ_Glast_H9_isch pJ

value: aNSC


title: FAD,rep1,Neg,Plate2,D4

value: MHCII+


title: Str_Glast_N17 pM


title: FAD,rep1,Neg,Plate2,D7


title: FAD,rep1,Neg,Plate2,E11


title: Str_Glast_N18 pM


title: Str_Glast_N21 pM


title: FAD,rep1,Neg,Plate2,D2


title: SVZ_Glast_H7_isch pJ


title: SVZ_Glast_H4_isch pJ


title: FAD,rep1,Neg,Plate2,D11

value: Adult Brain Homeostatic


title: FAD,rep1,Neg,Plate2,D1


title: FAD,rep1,Neg,Plate2,D12


title: FAD,rep1,Neg,Plate2,D3


title: SVZ_Glast_H3_isch pJ


title: Str_Glast_N16 pM

value: astrocyte (striatum)


title: Str_Glast_N15 pM


title: FAD,rep1,Neg,Plate2,C9

value: DAM 2


title: FAD,rep1,Neg,Plate2,C5

value: Neg


title: FAD,rep1,Neg,Plate2,C8


title: FAD,rep1,Neg,Plate2,C7


title: FAD,rep1,Neg,Plate2,C4

value: DAM 1


title: Str_Glast_N12 pM

value: TiCY


title: FAD,rep1,Neg,Plate2,C6


title: SVZ_Glast_H1_isch pJ

value: vSVZ astrocyte


title: FAD,rep1,Neg,Plate2,C2


title: FAD,rep1,Neg,Plate2,D5


title: SVZ_Glast_H2_isch pJ

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


title: SVZ_Glast_H18_isch pJ

value: neuroblast

value: 2 days post ischemia


title: Str_Glast_N11 pM


title: SVZ_Glast_H16_isch pJ


title: FAD,rep1,Neg,Plate2,C12

value: Brain


title: SVZ_Glast_H8_isch pJ


title: FAD,rep1,Neg,Plate2,D8

value: Isolated Microglia


title: FAD,rep1,Neg,Plate2,C3

value: IEG+


title: SVZ_Glast_H15_isch pJ

value: TAP


title: FAD,rep1,Neg,Plate2,C1

value: Early Postnatal Homeostatic

value: 4 months


title: Str_Glast_N14 pM

value: striatum & ventricular-subventricular zone

value: naive


title: FAD,rep1,Neg,Plate2,B8

value: PAM


title: FAD,rep1,Neg,Plate2,C11


title: Str_Glast_N10 pM

value: astrocyte (striatum)


title: FAD,rep1,Neg,Plate2,C10

value: Neg


title: FAD,rep1,Neg,Plate2,B5


title: FAD,rep1,Neg,Plate2,B9


title: Str_Glast_N13 pM


title: Str_Glast_N1 pM


title: SVZ_Glast_H14_isch pJ


title: Str_Glast_M8 pM


title: FAD,rep1,Neg,Plate2,B7


title: SVZ_Glast_H12_isch pJ


title: FAD,rep1,Neg,Plate2,B4

value: Adult Spinal Cord Homeostatic


title: FAD,rep1,Neg,Plate2,B3


title: FAD,rep1,Neg,Plate2,B2


title: Str_Glast_M6 pM

value: TiCY


title: SVZ_Glast_H11_isch pJ


title: FAD,rep1,Neg,Plate2,B12


title: FAD,rep1,Neg,Plate2,B6

value: Adult Brain Homeostatic


title: SVZ_Glast_G9_isch pJ

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


title: FAD,rep1,Neg,Plate2,B11

value: DAM 2


title: FAD,rep1,Neg,Plate2,B10


title: Str_Glast_M9 pM


title: SVZ_Glast_H10_isch pJ

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate2,A8

value: Brain


title: FAD,rep1,Neg,Plate2,A9

value: Isolated Microglia


title: Str_Glast_M4 pM


title: SVZ_Glast_G8_isch pJ

value: neuroblast


title: FAD,rep1,Neg,Plate2,A7


title: SVZ_Glast_H13_isch pJ

value: aNSC


title: Str_Glast_M3 pM


title: FAD,rep1,Neg,Plate2,A6

value: Early Postnatal Homeostatic


title: FAD,rep1,Neg,Plate2,A5

value: IEG+

value: 4 months


title: SVZ_Glast_G6_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_M24 pM

value: naive


title: Str_Glast_M23 pM

value: astrocyte (striatum)


title: Str_Glast_M7 pM


title: FAD,rep1,Neg,Plate2,A12

value: Neg


title: SVZ_Glast_G5_isch pJ


title: FAD,rep1,Neg,Plate2,A3


title: FAD,rep1,Neg,Plate2,A11


title: FAD,rep1,Neg,Plate2,A10


title: Str_Glast_M5 pM


title: FAD,rep1,Neg,Plate2,A1


title: Str_Glast_M21 pM


title: Str_Glast_M22 pM


title: SVZ_Glast_G18_isch pJ

value: vSVZ astrocyte


title: FAD,rep1,Neg,Plate1,G7


title: SVZ_Glast_G17_isch pJ


title: FAD,rep1,Neg,Plate1,G4


title: SVZ_Glast_G16_isch pJ


title: Str_Glast_M19 pM

value: TiCY


title: FAD,rep1,Neg,Plate1,G3


title: Str_Glast_M20 pM


title: FAD,rep1,Neg,Plate1,G2


title: SVZ_Glast_G1_isch pJ


title: FAD,rep1,Neg,Plate1,G1


title: SVZ_Glast_G14_isch pJ


title: Str_Glast_M18 pM


title: SVZ_Glast_G13_isch pJ


title: FAD,rep1,Neg,Plate1,F8


title: FAD,rep1,Neg,Plate2,A4


title: SVZ_Glast_G12_isch pJ


title: FAD,rep1,Neg,Plate1,F7


title: FAD,rep1,Neg,Plate1,F6

value: Adult Spinal Cord Homeostatic


title: FAD,rep1,Neg,Plate1,G8


title: FAD,rep1,Neg,Plate1,G9


title: FAD,rep1,Neg,Plate1,G6


title: FAD,rep1,Neg,Plate1,F4


title: FAD,rep1,Neg,Plate1,F5


title: Str_Glast_M16 pM


title: SVZ_Glast_G11_isch pJ

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


title: SVZ_Glast_G15_isch pJ


title: Str_Glast_M15 pM


title: FAD,rep1,Neg,Plate1,F3


title: Str_Glast_M14 pM


title: Str_Glast_M12 pM


title: SVZ_Glast_G10_isch pJ


title: SVZ_Glast_F9_isch pJ


title: FAD,rep1,Neg,Plate1,F2


title: Str_Glast_M17 pM


title: FAD,rep1,Neg,Plate1,F10


title: FAD,rep1,Neg,Plate1,F12


title: SVZ_Glast_F6_isch pJ


title: FAD,rep1,Neg,Plate1,F9


title: FAD,rep1,Neg,Plate1,F1


title: FAD,rep1,Neg,Plate1,F11


title: Str_Glast_M11 pM


title: FAD,rep1,Neg,Plate1,E9

value: DAM 2


title: Str_Glast_M2 pM


title: SVZ_Glast_F8_isch pJ

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate1,E8

value: Brain


title: FAD,rep1,Neg,Plate1,E5

value: Isolated Microglia


title: FAD,rep1,Neg,Plate1,E6


title: SVZ_Glast_F4_isch pJ

value: reactive astrocyte


title: SVZ_Glast_F5_isch pJ

value: neuroblast


title: Str_Glast_M1 pM


title: Str_Glast_M10 pM


title: FAD,rep1,Neg,Plate1,E4

value: Early Postnatal Homeostatic


title: FAD,rep1,Neg,Plate1,E3

value: IEG+


title: Str_Glast_L9 pM


title: FAD,rep1,Neg,Plate1,E2

value: Adult Brain Homeostatic

value: 4 months


title: SVZ_Glast_F18_isch pJ

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_F1_isch pJ


title: FAD,rep1,Neg,Plate1,E12

value: DAM 1


title: FAD,rep1,Neg,Plate1,E11

value: Neg


title: FAD,rep1,Neg,Plate1,E10


title: SVZ_Glast_F17_isch pJ

value: aNSC


title: FAD,rep1,Neg,Plate1,D8


title: Str_Glast_L8 pM

value: astrocyte (striatum)

value: TiCY

value: naive


title: Str_Glast_L4 pM


title: Str_Glast_L7 pM


title: FAD,rep1,Neg,Plate1,E1


title: FAD,rep1,Neg,Plate1,D4


title: Str_Glast_L6 pM


title: Str_Glast_L24 pM


title: FAD,rep1,Neg,Plate1,D9


title: SVZ_Glast_F16_isch pJ

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


title: FAD,rep1,Neg,Plate1,D12

value: DAM 2


title: FAD,rep1,Neg,Plate1,D7

value: Brain


title: FAD,rep1,Neg,Plate1,D11

value: Isolated Microglia


title: SVZ_Glast_F11_isch pJ

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate1,D6

value: Divding


title: SVZ_Glast_F14_isch pJ


title: Str_Glast_L22 pM


title: FAD,rep1,Neg,Plate1,C8

value: Early Postnatal Homeostatic


title: Str_Glast_L2 pM


title: SVZ_Glast_F13_isch pJ

value: neuroblast


title: Str_Glast_L3 pM


title: FAD,rep1,Neg,Plate1,D5


title: FAD,rep1,Neg,Plate1,D2


title: FAD,rep1,Neg,Plate1,C6

value: IEG+


title: SVZ_Glast_F12_isch pJ


title: FAD,rep1,Neg,Plate1,D3

value: 4 months


title: FAD,rep1,Neg,Plate1,D10


title: Str_Glast_L21 pM

value: striatum & ventricular-subventricular zone


title: FAD,rep1,Neg,Plate1,C9


title: SVZ_Glast_F10_isch pJ

value: vSVZ astrocyte


title: FAD,rep1,Neg,Plate1,C4

value: MHCII+

value: Neg


title: SVZ_Glast_E9_isch pJ

value: aNSC


title: FAD,rep1,Neg,Plate1,C2


title: FAD,rep1,Neg,Plate1,C7

value: PAM


title: Str_Glast_L19 pM

value: astrocyte (striatum)

value: TiCY

value: naive


title: FAD,rep1,Neg,Plate1,C5

value: Brain


title: Str_Glast_L16 pM


title: FAD,rep1,Neg,Plate1,C10

value: Isolated Microglia


title: Str_Glast_L15 pM


title: SVZ_Glast_E8_isch pJ

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

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate1,C1

value: DAM 2


title: SVZ_Glast_E17_isch pJ


title: FAD,rep1,Neg,Plate1,C3


title: SVZ_Glast_E6_isch pJ


title: FAD,rep1,Neg,Plate1,C11

value: Early Postnatal Homeostatic


title: FAD,rep1,Neg,Plate1,B6

value: DAM 1


title: SVZ_Glast_E4_isch pJ

value: neuroblast


title: SVZ_Glast_E18_isch pJ

value: striatum & ventricular-subventricular zone


title: FAD,rep1,Neg,Plate1,B9

value: Adult Spinal Cord Homeostatic

value: 4 months


title: FAD,rep1,Neg,Plate1,B8

value: Neg


title: FAD,rep1,Neg,Plate1,B7


title: SVZ_Glast_E16_isch pJ


title: Str_Glast_L1 pM


title: FAD,rep1,Neg,Plate1,B10


title: FAD,rep1,Neg,Plate1,B5


title: SVZ_Glast_E13_isch pJ

value: reactive astrocyte


title: FAD,rep1,Neg,Plate1,B4


title: SVZ_Glast_E15_isch pJ

value: vSVZ astrocyte


title: Str_Glast_L17 pM

value: astrocyte (striatum)


title: FAD,rep1,Neg,Plate1,B3


title: EAE,rep1,Pos,Plate2,H7

source_name: Spinal Cord

value: Spinal Cord

value: IEG+

value: EAE

value: 2 months

value: Pos


title: Str_Glast_L10 pM

value: TiCY

value: naive


title: EAE,rep1,Pos,Plate2,H5

value: Isolated Microglia

value: MHCII+


title: FAD,rep1,Neg,Plate1,B2

value: Brain


title: SVZ_Glast_D9_isch pJ

value: striatum & ventricular-subventricular zone

value: TAP

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

value: 2 days post ischemia


title: FAD,rep1,Neg,Plate1,B1

value: DAM 1

value: 4 months

value: Neg


title: SVZ_Glast_E14_isch pJ


title: EAE,rep1,Pos,Plate2,H9

value: Spinal Cord


title: EAE,rep1,Pos,Plate2,H8


title: Str_Glast_K3 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,H10

value: EAE


title: Str_Glast_K9 pM


title: SVZ_Glast_E11_isch pJ

value: neuroblast


title: Str_Glast_L14 pM


title: EAE,rep1,Pos,Plate2,G7

value: Adult Spinal Cord Homeostatic

value: 2 months

value: Pos


title: Str_Glast_L13 pM

value: TiCY

value: naive


title: EAE,rep1,Pos,Plate2,H6

value: Isolated Microglia

value: Adult Brain Homeostatic


title: SVZ_Glast_D2_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_L12 pM


title: EAE,rep1,Pos,Plate2,H11

value: MHCII+


title: EAE,rep1,Pos,Plate2,H4


title: EAE,rep1,Pos,Plate2,H3

value: IEG+


title: Str_Glast_K4 pM


title: Str_Glast_K5 pM


title: EAE,rep1,Pos,Plate2,G5

value: DAM 2


title: SVZ_Glast_D8_isch pJ

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

value: 2 days post ischemia


title: EAE,rep1,Pos,Plate2,G4

value: Spinal Cord


title: EAE,rep1,Pos,Plate2,G8


title: Str_Glast_K23 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,H2

value: EAE


title: SVZ_Glast_D5_isch pJ

value: neuroblast


title: EAE,rep1,Pos,Plate2,H12


title: Str_Glast_K24 pM


title: Str_Glast_K2 pM


title: SVZ_Glast_D14_isch pJ

value: aNSC


title: EAE,rep1,Pos,Plate2,H1

value: 2 months


title: EAE,rep1,Pos,Plate2,G10

value: Pos


title: SVZ_Glast_D13_isch pJ

value: vSVZ astrocyte


title: EAE,rep1,Pos,Plate2,G1

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Pos,Plate2,G9

value: Isolated Microglia


title: SVZ_Glast_D12_isch pJ


title: SVZ_Glast_D1_isch pJ


title: EAE,rep1,Pos,Plate2,G6


title: Str_Glast_K22 pM

value: TiCY

value: naive


title: SVZ_Glast_D16_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_K17 pM


title: EAE,rep1,Pos,Plate2,F8

value: MHCII+


title: Str_Glast_K7 pM


title: EAE,rep1,Pos,Plate2,F7


title: Str_Glast_K21 pM


title: SVZ_Glast_D15_isch pJ


title: EAE,rep1,Pos,Plate2,F6


title: EAE,rep1,Pos,Plate2,G3

value: DAM 2


title: SVZ_Glast_D17_isch pJ

value: TAP

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


title: Str_Glast_K20 pM


title: EAE,rep1,Pos,Plate2,F3

value: Spinal Cord


title: EAE,rep1,Pos,Plate2,G2


title: Str_Glast_K19 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,G12

value: IEG+

value: EAE


title: EAE,rep1,Pos,Plate2,G11


title: SVZ_Glast_C7_isch pJ

value: 2 days post ischemia


title: EAE,rep1,Pos,Plate2,F10

value: 2 months


title: SVZ_Glast_C6_isch pJ


title: EAE,rep1,Pos,Plate2,F9

value: Pos


title: EAE,rep1,Pos,Plate2,F11


title: Str_Glast_K16 pM


title: SVZ_Glast_D11_isch pJ


title: Str_Glast_K11 pM


title: SVZ_Glast_C3_isch pJ


title: EAE,rep1,Pos,Plate2,F5


title: SVZ_Glast_D10_isch pJ

value: neuroblast


title: EAE,rep1,Pos,Plate2,E7


title: Str_Glast_K15 pM


title: Str_Glast_K14 pM


title: SVZ_Glast_C9_isch pJ

value: aNSC


title: EAE,rep1,Pos,Plate2,F4

value: Isolated Microglia


title: SVZ_Glast_C8_isch pJ


title: EAE,rep1,Pos,Plate2,F2


title: EAE,rep1,Pos,Plate2,E5


title: EAE,rep1,Pos,Plate2,F1


title: Str_Glast_K12 pM

value: TiCY


title: EAE,rep1,Pos,Plate2,E4


title: Str_Glast_K13 pM

value: naive


title: SVZ_Glast_C1_isch pJ

value: striatum & ventricular-subventricular zone


title: EAE,rep1,Pos,Plate2,E3

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Pos,Plate2,E9

value: MHCII+


title: EAE,rep1,Pos,Plate2,E8


title: Str_Glast_J9 pM


title: EAE,rep1,Pos,Plate2,E2

value: DAM 2


title: SVZ_Glast_C18_isch pJ

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


title: EAE,rep1,Pos,Plate2,E12

value: Spinal Cord


title: Str_Glast_K10 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,F12


title: EAE,rep1,Pos,Plate2,E10


title: Str_Glast_J4 pM


title: EAE,rep1,Pos,Plate2,E6

value: IEG+


title: SVZ_Glast_C2_isch pJ

value: TAP


title: SVZ_Glast_C14_isch pJ

value: 2 days post ischemia


title: SVZ_Glast_C13_isch pJ


title: EAE,rep1,Pos,Plate2,D6

value: EAE

value: 2 months


title: EAE,rep1,Pos,Plate2,D9

value: Pos


title: Str_Glast_J20 pM


title: EAE,rep1,Pos,Plate2,D4


title: EAE,rep1,Pos,Plate2,D7


title: EAE,rep1,Pos,Plate2,D2


title: SVZ_Glast_C11_isch pJ

value: neuroblast


title: Str_Glast_K1 pM


title: EAE,rep1,Pos,Plate2,D12

value: Isolated Microglia


title: Str_Glast_J18 pM

value: TiCY


title: SVZ_Glast_B8_isch pJ

value: aNSC


title: EAE,rep1,Pos,Plate2,C9


title: Str_Glast_J6 pM

value: striatum & ventricular-subventricular zone

value: naive


title: EAE,rep1,Pos,Plate2,E11


title: EAE,rep1,Pos,Plate2,C8


title: EAE,rep1,Pos,Plate2,C7

value: DAM 1


title: SVZ_Glast_C17_isch pJ


title: EAE,rep1,Pos,Plate2,E1

value: Early Postnatal Homeostatic


title: EAE,rep1,Pos,Plate2,C6


title: Str_Glast_J5 pM


title: SVZ_Glast_C15_isch pJ

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


title: Str_Glast_J13 pM


title: EAE,rep1,Pos,Plate2,C4

value: Spinal Cord

value: DAM 2


title: SVZ_Glast_B1_isch pJ


title: EAE,rep1,Pos,Plate2,D8

value: IEG+


title: EAE,rep1,Pos,Plate2,C3


title: Str_Glast_J23 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,D5

value: MHCII+


title: Str_Glast_J12 pM


title: EAE,rep1,Pos,Plate2,C10

value: Adult Spinal Cord Homeostatic

value: EAE


title: Str_Glast_GFP+_D8 pL

source_name: cerebral cortex & striatum

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: EAE,rep1,Pos,Plate2,D3

value: Isolated Microglia

value: 2 months

value: Pos


title: EAE,rep1,Pos,Plate2,C1


title: EAE,rep1,Pos,Plate2,B9


title: Str_Glast_J22 pM

value: striatum & ventricular-subventricular zone

value: TiCY


title: Str_Glast_J19 pM

value: naive


title: EAE,rep1,Pos,Plate2,D11


title: SVZ_Glast_B9_isch pJ

value: 2 days post ischemia


title: EAE,rep1,Pos,Plate2,D10


title: EAE,rep1,Pos,Plate2,B6


title: SVZ_Glast_B13_isch pJ

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


title: EAE,rep1,Pos,Plate2,D1

value: Spinal Cord


title: EAE,rep1,Pos,Plate2,B5

value: DAM 2


title: SVZ_Glast_C12_isch pJ

value: TAP


title: Str_Glast_J17 pM

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,B4

value: IEG+


title: Str_Glast_J15 pM


title: EAE,rep1,Pos,Plate2,B2


title: SVZ_Glast_B7_isch pJ


title: SVZ_Glast_B11_isch pJ

value: aNSC


title: SVZ_Glast_B6_isch pJ


title: EAE,rep1,Pos,Plate2,C2

value: MHCII+

value: EAE


title: SVZ_Glast_B18_isch pJ

value: neuroblast


title: EAE,rep1,Pos,Plate2,C5

value: Isolated Microglia

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Pos,Plate2,B10

value: 2 months

value: Pos


title: EAE,rep1,Pos,Plate2,C12


title: Str_Glast_GFP+_D9 pL

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: EAE,rep1,Pos,Plate2,B1


title: EAE,rep1,Pos,Plate2,C11


title: SVZ_Glast_B17_isch pJ

value: striatum & ventricular-subventricular zone

value: 2 days post ischemia


title: EAE,rep1,Pos,Plate2,A8

value: Spinal Cord


title: SVZ_Glast_A7_isch pJ

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


title: Str_Glast_GFP+_D7 pL

value: naive


title: EAE,rep1,Pos,Plate2,A7


title: EAE,rep1,Pos,Plate2,B8


title: SVZ_Glast_B15_isch pJ


title: SVZ_Glast_B14_isch pJ

value: reactive astrocyte


title: Str_Glast_GFP+_D6 pL

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate2,B7

value: DAM 2


title: SVZ_Glast_B12_isch pJ

value: TAP


title: Str_Glast_GFP+_C6 pL


title: Str_Glast_GFP+_D11 pL


title: EAE,rep1,Pos,Plate2,A5

value: MHCII+

value: EAE


title: EAE,rep1,Pos,Plate2,A6

value: Isolated Microglia


title: EAE,rep1,Pos,Plate2,B3

value: IEG+


title: Str_Glast_GFP+_D10 pL


title: SVZ_Glast_A5_isch pJ

value: neuroblast


title: Str_Glast_GFP+_C8 pL


title: EAE,rep1,Pos,Plate2,A3

value: 2 months

value: Pos


title: EAE,rep1,Pos,Plate2,A2

value: DAM 1


title: SVZ_Glast_A9_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_GFP+_D1 pL

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: EAE,rep1,Pos,Plate2,B12

value: Spinal Cord


title: SVZ_Glast_A8_isch pJ

value: vSVZ astrocyte

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

value: 2 days post ischemia


title: Str_Glast_GFP+_C4 pL

value: astrocyte (striatum)

value: naive


title: Str_Glast_GFP+_C9 pL


title: EAE,rep1,Pos,Plate2,A9

value: MHCII+


title: Str_Glast_GFP+_C2 pL


title: EAE,rep1,Pos,Plate2,A1

value: EAE


title: EAE,rep1,Pos,Plate2,A10

value: Isolated Microglia


title: Str_Glast_GFP+_C7 pL


title: SVZ_Glast_A6_isch pJ


title: EAE,rep1,Pos,Plate2,B11

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Pos,Plate1,H9


title: EAE,rep1,Pos,Plate1,H7

value: IEG+


title: EAE,rep1,Pos,Plate2,A4

value: 2 months


title: EAE,rep1,Pos,Plate1,H8

value: Pos


title: SVZ_Glast_A2_isch pJ

value: neuroblast


title: EAE,rep1,Pos,Plate1,H5


title: SVZ_Glast_A1_isch pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_GFP+_B9 pL

value: cerebral cortex & striatum


title: EAE,rep1,Pos,Plate1,H3


title: Str_Glast_GFP+_C3 pL

value: WT (TCF-Lef reporter)


title: EAE,rep1,Pos,Plate1,H6

value: Spinal Cord


title: Str_Glast_GFP+_C11 pL


title: EAE,rep1,Pos,Plate2,A12


title: SVZ_Glast_A14_isch pJ


title: EAE,rep1,Pos,Plate1,H12


title: Str_Glast_GFP+_B6 pL


title: SVZ_Glast_A13_isch pJ


title: EAE,rep1,Pos,Plate1,H4


title: SVZ_Glast_A16_isch pJ

value: TAP


title: SVZ_Glast_A18_isch pJ

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


title: EAE,rep1,Pos,Plate1,H11


title: EAE,rep1,Pos,Plate1,H2


title: EAE,rep1,Pos,Plate2,A11


title: EAE,rep1,Pos,Plate1,H10


title: SVZ_Glast_A17_isch pJ

value: aNSC

value: 2 days post ischemia


title: EAE,rep1,Pos,Plate1,G8


title: SVZ_Glast_A15_isch pJ

value: vSVZ astrocyte


title: Str_Glast_GFP+_B8 pL

value: astrocyte (striatum)

value: naive


title: Str_Glast_GFP+_C10 pL


title: Str_Glast_GFP+_B3 pL


title: Str_Glast_GFP+_B5 pL


title: EAE,rep1,Pos,Plate1,G7

value: Isolated Microglia

value: DAM 2

value: EAE


title: SVZ_Glast_A12_isch pJ


title: EAE,rep1,Pos,Plate1,G5

value: MHCII+

value: 2 months


title: EAE,rep1,Pos,Plate1,H1

value: Pos


title: SVZ_Glast_A11_isch pJ

value: striatum & ventricular-subventricular zone


title: EAE,rep1,Pos,Plate1,G6

value: IEG+


title: Str_Glast_GFP+_B10 pL

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: Str_Glast_P9_naive pJ

value: IFN(A/G)R KO


title: EAE,rep1,Pos,Plate1,G2

value: Spinal Cord


title: EAE,rep1,Pos,Plate1,G4


title: Str_Glast_GFP+_B2 pL


title: Str_Glast_P18_naive pJ


title: Str_Glast_GFP+_B1 pL


title: EAE,rep1,Pos,Plate1,G3

value: Adult Spinal Cord Homeostatic


title: Str_Glast_P17_naive pJ


title: Str_Glast_GFP+_A9 pL


title: EAE,rep1,Pos,Plate1,G10


title: EAE,rep1,Pos,Plate1,F9


title: EAE,rep1,Pos,Plate1,G11


title: EAE,rep1,Pos,Plate1,F8


title: EAE,rep1,Pos,Plate1,G1


title: Str_Glast_P13_naive pJ


title: EAE,rep1,Pos,Plate1,G9


title: Str_Glast_GFP+_A4 pL


title: Str_Glast_P16_naive pJ


title: Str_Glast_P15_naive pJ


title: EAE,rep1,Pos,Plate1,F5


title: Str_Glast_GFP+_A8 pL


title: EAE,rep1,Pos,Plate1,F6


title: EAE,rep1,Pos,Plate1,F3


title: Str_Glast_GFP+_A5 pL


title: EAE,rep1,Pos,Plate1,F7


title: EAE,rep1,Pos,Plate1,F4


title: Str_Glast_P11_naive pJ


title: Str_Glast_GFP+_A12 pL


title: EAE,rep1,Pos,Plate1,G12


title: Str_Glast_O9_naive pJ


title: EAE,rep1,Pos,Plate1,F2


title: Str_Glast_GFP+_A3 pL


title: EAE,rep1,Pos,Plate1,F12


title: Str_Glast_GFP+_A10 pL


title: EAE,rep1,Pos,Plate1,F11


title: Str_Glast_O16_naive pJ


title: Str_Glast_O17_naive pJ


title: Str_Glast_O8_naive pJ


title: Str_Glast_O7_naive pJ


title: EAE,rep1,Pos,Plate1,F1


title: Str_Glast_GFP+_A11 pL


title: EAE,rep1,Pos,Plate1,F10


title: Str_Glast_O14_naive pJ


title: Str_Glast_GFP+_B4 pL


title: Ctx_Glast_P10 pL

value: astrocyte (cortex)


title: Ctx_Glast_GFP+_L8 pL


title: EAE,rep1,Pos,Plate1,E4


title: EAE,rep1,Pos,Plate1,E3


title: EAE,rep1,Pos,Plate1,E6


title: EAE,rep1,Pos,Plate1,E2


title: EAE,rep1,Pos,Plate1,E8


title: EAE,rep1,Pos,Plate1,E7


title: EAE,rep1,Pos,Plate1,E5


title: EAE,rep1,Pos,Plate1,E9


title: EAE,rep1,Pos,Plate1,E10


title: Str_Glast_O11_naive pJ


title: Str_Glast_O15_naive pJ


title: Ctx_Glast_GFP+_L7 pL


title: Ctx_Glast_GFP+_L3 pL


title: Ctx_Glast_GFP+_L4 pL


title: Str_Glast_O18_naive pJ


title: EAE,rep1,Pos,Plate1,E12


title: EAE,rep1,Pos,Plate1,E11


title: EAE,rep1,Pos,Plate1,E1


title: EAE,rep1,Pos,Plate1,D8


title: EAE,rep1,Pos,Plate1,D9


title: Str_Glast_O10_naive pJ


title: Str_Glast_N8_naive pJ


title: EAE,rep1,Pos,Plate1,D7


title: Ctx_Glast_GFP+_L2 pL


title: EAE,rep1,Pos,Plate1,D6


title: Str_Glast_N7_naive pJ


title: Ctx_Glast_GFP+_L11 pL


title: EAE,rep1,Pos,Plate1,D5


title: Ctx_Glast_GFP+_L10 pL


title: EAE,rep1,Pos,Plate1,D4


title: EAE,rep1,Pos,Plate1,D2


title: Str_Glast_N18_naive pJ


title: EAE,rep1,Pos,Plate1,D3


title: EAE,rep1,Pos,Plate1,D12


title: Str_Glast_N17_naive pJ


title: Ctx_Glast_GFP+_K8 pL


title: EAE,rep1,Pos,Plate1,D1


title: Ctx_Glast_GFP+_K6 pL


title: EAE,rep1,Pos,Plate1,D11


title: Str_Glast_N16_naive pJ


title: EAE,rep1,Pos,Plate1,D10


title: EAE,rep1,Pos,Plate1,C7


title: Str_Glast_N13_naive pJ


title: EAE,rep1,Pos,Plate1,C8


title: EAE,rep1,Pos,Plate1,C9


title: Ctx_Glast_GFP+_K4 pL


title: Str_Glast_N12_naive pJ


title: EAE,rep1,Pos,Plate1,C6


title: EAE,rep1,Pos,Plate1,C3


title: EAE,rep1,Pos,Plate1,C4


title: Ctx_Glast_GFP+_K3 pL


title: EAE,rep1,Pos,Plate1,C5


title: Ctx_Glast_GFP+_L1 pL


title: Ctx_Glast_GFP+_K7 pL


title: Ctx_Glast_GFP+_K2 pL


title: Str_Glast_N15_naive pJ


title: Str_Glast_N10_naive pJ


title: EAE,rep1,Pos,Plate1,C2

value: DAM 1


title: EAE,rep1,Pos,Plate1,C12


title: Ctx_Glast_GFP+_K12 pL


title: Str_Glast_M9_naive pJ

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate1,C10


title: Ctx_Glast_GFP+_K10 pL

value: naive


title: EAE,rep1,Pos,Plate1,C1

value: Isolated Microglia


title: Ctx_Glast_GFP+_K1 pL


title: EAE,rep1,Pos,Plate1,B9


title: Str_Glast_M7_naive pJ


title: EAE,rep1,Pos,Plate1,B6

value: DAM 2


title: Ctx_Glast_GFP+_J7 pL


title: Str_Glast_N11_naive pJ


title: Str_Glast_M16_naive pJ


title: EAE,rep1,Pos,Plate1,B5

value: EAE


title: EAE,rep1,Pos,Plate1,B4


title: Ctx_Glast_GFP+_J3 pL


title: Ctx_Glast_GFP+_J5 pL


title: EAE,rep1,Pos,Plate1,B12

value: MHCII+


title: EAE,rep1,Pos,Plate1,B2

value: 2 months


title: EAE,rep1,Pos,Plate1,B11

value: Pos


title: Ctx_Glast_GFP+_J2 pL


title: EAE,rep1,Pos,Plate1,C11


title: Str_Glast_M12_naive pJ

value: striatum & ventricular-subventricular zone


title: Ctx_Glast_GFP+_J10 pL


title: EAE,rep1,Pos,Plate1,B8


title: Str_Glast_M17_naive pJ


title: EAE,rep1,Pos,Plate1,A8

value: IEG+


title: Str_Glast_M11_naive pJ


title: Str_Glast_M10_naive pJ


title: EAE,rep1,Pos,Plate1,B10


title: EAE,rep1,Pos,Plate1,B1


title: EAE,rep1,Pos,Plate1,A9


title: EAE,rep1,Pos,Plate1,A7


title: Str_Glast_KO2_P9 pJ

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

value: 2 days post ischemia


title: Ctx_Glast_GFP+_I8 pL

value: cerebral cortex & striatum

value: WT (TCF-Lef reporter)


title: EAE,rep1,Pos,Plate1,B3

value: Spinal Cord


title: Str_Glast_M14_naive pJ

value: IFN(A/G)R KO


title: EAE,rep1,Pos,Plate1,A5


title: Ctx_Glast_GFP+_I6 pL

value: astrocyte (cortex)


title: EAE,rep1,Pos,Plate1,A4


title: Str_Glast_KO2_P8 pJ

value: astrocyte (striatum)


title: EAE,rep1,Pos,Plate1,A3

value: DAM 1


title: Ctx_Glast_GFP+_I5 pL

value: naive


title: Str_Glast_KO2_P6 pJ


title: EAE,rep1,Pos,Plate1,A10

value: Isolated Microglia


title: Ctx_Glast_GFP+_I4 pL


title: EAE,rep1,Pos,Plate1,A2

value: EAE


title: Str_Glast_KO2_P7 pJ


title: EAE,rep1,Pos,Plate1,A11

value: MHCII+


title: Str_Glast_KO2_P4 pJ

value: neurogenic striatal astrocyte


title: EAE,rep1,Pos,Plate1,A1

value: 2 months

value: Pos


title: EAE,rep1,Neg,Plate2,H6

value: Adult Spinal Cord Homeostatic

value: Neg


title: EAE,rep1,Neg,Plate2,H5


title: Ctx_Glast_GFP+_I11 pL


title: EAE,rep1,Neg,Plate2,H9

value: Transitional DAM


title: Ctx_Glast_GFP+_I1 pL

value: cerebral cortex & striatum


title: EAE,rep1,Neg,Plate2,H7


title: Ctx_Glast_GFP+_I12 pL

value: WT (TCF-Lef reporter)


title: EAE,rep1,Neg,Plate2,H3

value: Spinal Cord

value: IEG+


title: EAE,rep1,Neg,Plate2,H2


title: EAE,rep1,Neg,Plate2,H12


title: Str_Glast_KO2_P10 pJ

value: striatum & ventricular-subventricular zone

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

value: 2 days post ischemia


title: EAE,rep1,Neg,Plate2,H11


title: Str_Glast_KO2_P2 pJ

value: reactive astrocyte


title: EAE,rep1,Neg,Plate2,H10

value: Isolated Microglia

value: DAM 2


title: Ctx_Glast_GFP+_I7 pL

value: astrocyte (cortex)

value: naive


title: Str_Glast_KO2_O8 pJ

value: astrocyte (striatum)


title: EAE,rep1,Neg,Plate2,G9

value: EAE

value: 2 months


title: Str_Glast_KO2_P12 pJ


title: Ctx_Glast_GFP+_I10 pL


title: EAE,rep1,Pos,Plate1,A12

value: Pos


title: EAE,rep1,Neg,Plate2,G7

value: Neg


title: SVZ_Glast_522 pI

value: TiCY


title: Str_Glast_KO2_O4 pJ


title: EAE,rep1,Neg,Plate2,G5


title: SVZ_Glast_640 pI


title: SVZ_Glast_566 pI


title: EAE,rep1,Neg,Plate2,G2

value: Adult Spinal Cord Homeostatic


title: SVZ_Glast_460 pI


title: EAE,rep1,Neg,Plate2,H1

value: Spinal Cord


title: Str_Glast_KO2_O6 pJ


title: Str_Glast_KO2_O11 pJ


title: EAE,rep1,Neg,Plate2,G8

value: IEG+


title: Str_Glast_KO2_P11 pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_KO2_N2 pJ

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


title: EAE,rep1,Neg,Plate2,G12


title: Str_Glast_88 pI

value: 2 days post ischemia


title: EAE,rep1,Neg,Plate2,G10


title: Str_Glast_KO2_N12 pJ


title: SVZ_Glast_485 pI


title: Str_Glast_KO2_O3 pJ


title: EAE,rep1,Neg,Plate2,G6

value: DAM 1


title: Str_Glast_43 pI

value: reactive astrocyte


title: EAE,rep1,Neg,Plate2,G4

value: Isolated Microglia


title: EAE,rep1,Neg,Plate2,G3


title: Str_Glast_96 pI

value: neurogenic striatal astrocyte


title: Str_Glast_297 pI


title: Str_Glast_KO2_N10 pJ


title: EAE,rep1,Neg,Plate2,G11


title: EAE,rep1,Neg,Plate2,G1


title: EAE,rep1,Neg,Plate2,F4


title: EAE,rep1,Neg,Plate2,F5

value: Adult Brain Homeostatic


title: Str_Glast_KO2_N1 pJ


title: Str_Glast_KO2_N11 pJ

value: astrocyte (striatum)


title: EAE,rep1,Neg,Plate2,F9

value: EAE


title: EAE,rep1,Neg,Plate2,F12

value: 2 months


title: EAE,rep1,Neg,Plate2,F6


title: EAE,rep1,Neg,Plate2,F7

value: MHCII+


title: Str_Glast_274 pI


title: Str_Glast_KO2_M7 pJ


title: Str_Glast_293 pI


title: EAE,rep1,Neg,Plate2,F1

value: Neg


title: Str_Glast_193 pI

value: TiCY


title: EAE,rep1,Neg,Plate2,F3


title: Str_Glast_287 pI


title: Str_Glast_174 pI


title: Str_Glast_KO2_M6 pJ


title: EAE,rep1,Neg,Plate2,F2


title: Str_Glast_KO2_M8 pJ


title: EAE,rep1,Neg,Plate2,F10


title: EAE,rep1,Neg,Plate2,E8

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Neg,Plate2,F11

value: Spinal Cord


title: EAE,rep1,Neg,Plate2,E9


title: EAE,rep1,Neg,Plate2,E5

value: IEG+


title: Str_Glast_KO2_M4 pJ

value: striatum & ventricular-subventricular zone


title: EAE,rep1,Neg,Plate2,E7


title: Str_Glast_119 pI


title: Str_Glast_KO2_M3 pJ

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


title: EAE,rep1,Neg,Plate2,E4


title: Str_Glast_154 pI

value: 2 days post ischemia


title: Str_Glast_KO2_M1 pJ


title: Str_Glast_104 pI


title: Str_Glast_KO2_M12 pJ


title: EAE,rep1,Neg,Plate2,E3


title: EAE,rep1,Neg,Plate2,E2


title: EAE,rep1,Neg,Plate2,E10


title: EAE,rep1,Neg,Plate2,D8


title: EAE,rep1,Neg,Plate2,E12


title: Str_Glast_KO2_L5 pJ


title: EAE,rep1,Neg,Plate2,E11


title: Str_Glast_158 pI


title: Str_Glast_KO2_L9 pJ


title: EAE,rep1,Neg,Plate2,E1

value: DAM 2


title: EAE,rep1,Neg,Plate2,D6


title: EAE,rep1,Neg,Plate2,D9


title: Str_Glast_KO2_L8 pJ

value: reactive astrocyte


title: Str_Glast_KO2_L4 pJ


title: EAE,rep1,Neg,Plate2,D7

value: Isolated Microglia


title: EAE,rep1,Neg,Plate2,E6


title: EAE,rep1,Neg,Plate2,D4


title: MEL, pol2ser5, Myrlin KD2

city: Bethesda

first: Ann

last: Dean

state: MD

address: 50 South Drive, Bldg 50

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
raw fastq files were preprocessed with cutadapt (v2.7).
ChIP-seq reads were aligned to the GRCm38 genome using Bowtie2 version 2.3.5, with the settings "--local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 --no-unal"
final reads were retained after removing non-uniquely mapped reads using samtools (v1.9) and duplicated reads using picard (v2.21.4) MarkDuplicates.
bigWig files were generated using the deepTools (v3.3.1) bamCoverage tool with "--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300"
Peaks were called using MACS v2.2.7.1 with default settings.
Assembly: Gencode M18 (GRCm38/mm10)
Supplementary files format and content: bigWig
Supplementary files format and content: peaks (MACS2 narrowPeak format)
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: MEL

growth_protocol: Control and CRISPR-edited mouse erythroid leukemia (MEL) cell lines were cultured in a 5% CO2 humidified incubator at 37 °C in DMEM with L-Glutamine, 10% fetal bovine serum, 1% Penicillin and Streptomycin and 1mM sodium pyruvate.

extract_protocol:
1M of Mel cells were collected for each biological replicate
CUT&Tag libraries were prepared using the CUT&Tag-IT™ Assay Kit (Active Motif, 53160) following to the manufacturer's protocol. 1M of Mel cells were collected for each biological replicate and two replicates were prepared. The Mel cells were bound to Concanavalin A Beads and Incubated with 1:50 rabbit polyclonal Phospho-Rpb1 CTD Ser5 and Ser2 antibody

value: MEL

value: mouse erythroid leukemia

value: Myrlin KD

tag: antibody

value: Phospho-Rpb1 CTD Ser5 (D9N5I, Cell signaling_13523)


title: MEL, pol2ser5, Myrlin KD1


title: MEL, pol2ser2, Myrlin KD2

value: Phospho-Rpb1 CTD Ser2 (E1Z3G, Cell signaling_13499)


title: EAE,rep1,Neg,Plate2,D5

value: EAE

value: 2 months


title: Str_Glast_KO2_L3 pJ

value: astrocyte (striatum)


title: MEL, pol2ser2, Myrlin KD1


title: SVZ_Glast_96 pH

value: TiCY

value: 21 days post ischemia


title: EAE,rep1,Neg,Plate2,D2

value: Spinal Cord

value: MHCII+

value: Neg


title: EAE,rep1,Neg,Plate2,H4

value: IEG+


title: Str_Glast_KO2_L12 pJ

value: striatum & ventricular-subventricular zone

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

value: 2 days post ischemia


title: MEL, pol2ser5, Ctrl2

value: MEL

value: dCAS control


title: EAE,rep1,Neg,Plate2,D3

value: Isolated Microglia


title: EAE,rep1,Neg,Plate2,D11

value: Adult Spinal Cord Homeostatic


title: Str_Glast_KO2_L10 pJ


title: MEL, pol2ser5, Ctrl1

value: mouse erythroid leukemia

value: Phospho-Rpb1 CTD Ser5 (D9N5I, Cell signaling_13523)


title: EAE,rep1,Neg,Plate2,D1

value: EAE

value: 2 months


title: Str_Glast_KO2_K8 pJ

value: astrocyte (striatum)


title: MEL, pol2ser2, Ctrl2

value: Phospho-Rpb1 CTD Ser2 (E1Z3G, Cell signaling_13499)


title: EAE,rep1,Neg,Plate2,C9

value: Spinal Cord


title: EAE,rep1,Neg,Plate2,C7


title: EAE,rep1,Neg,Plate2,D10


title: EAE,rep1,Neg,Plate2,C8


title: EAE,rep1,Neg,Plate2,C6


title: MEL, pol2ser2, Ctrl1


title: Str_Glast_KO2_K7 pJ


title: Str_Glast_KO2_K2 pJ

value: neurogenic striatal astrocyte


title: EAE,rep1,Neg,Plate2,D12

value: Neg


title: EAE,rep1,Neg,Plate2,C4

value: IEG+


title: detc

city: Boston

first: Isabela

middle: J

last: Kernin

state: MA

address: 55 Fruit St

department: Center for Immunology and Inflammatory Diseases

institute: Massachusetts General Hospital

data_processing:
Raw sequencing data was pre-processed with CellRanger (v6.1.2, 10X Genomics) to demultiplex FASTQ reads, align reads to the mouse reference genome (mm10, v2020-A from 10x Genomics), and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: mm10 (v2020-A from 10x Genomics)
Supplementary files format and content: The raw count matrix files are in .h5 format and include the UMI counts and sample ID information for each cell

molecule: polyA RNA

source_name: skin

extract_protocol:
A single-cell suspension of skin cells was generated from 30 pooled WT mice. Dermal gd T cells, DETCs, and GD3 cells were FACS sorted into 50% fully-supplemented RPMI and 50% FBS. After washing the sorted cells in FACS Buffer, each population was loaded as a separate channel on the Chromium 10x Genomic v1.1 platform (10X Genomics).
Libraries were prepared using the Chromium Single Cell 5' Library Construction Kit and generated from the cDNA produced through the Chromium chemistry. Nucleic acid products were separated using SPRIselect beads (Beckman Coulter). Libraries were quantified using the Bioanalyer High Sensitivity DNA analysis kit (Agilent). Sequencing of GEX libraries was performed using the Nextseq 500/550 High Output kit v2.5 (75 cycles; Illumina) and sequencing was performed on the NextSeq 550 (Illumina).

value: skin

value: WT

value: DETC (dendritic epidermal) gamma-delta T-cell


title: EAE,rep1,Neg,Plate2,C12


title: Str_Glast_KO2_J8 pJ

value: striatum & ventricular-subventricular zone

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

value: 2 days post ischemia


title: EAE,rep1,Neg,Plate2,C3

value: Isolated Microglia


title: EAE,rep1,Neg,Plate2,C5

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Neg,Plate2,C1

value: Adult Brain Homeostatic


title: gd3_B

value: GD3 gamma-delta T-cell


title: EAE,rep1,Neg,Plate2,B8

value: EAE

value: 2 months


title: gd3_A


title: Str_Glast_KO2_J5 pJ

value: astrocyte (striatum)


title: Str_Glast_KO2_K3 pJ

value: reactive astrocyte


title: EAE,rep1,Neg,Plate2,C10

value: Spinal Cord

value: MHCII+


title: dermal

value: Dermal gamma-delta T-cell


title: EAE,rep1,Neg,Plate2,B9

value: Neg


title: Str_Glast_KO2_J6 pJ


title: EAE,rep1,Neg,Plate2,B5


title: EAE,rep1,Neg,Plate2,C11

value: IEG+


title: EAE,rep1,Neg,Plate2,B7


title: ind8hpe_mesophyllum_settled_larva_7_48

city: Brisbane

first: Tahsha

last: Say

state: QLD

address: The University of Queensland

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

description: Transcriptomic data for a total of 144 individual swimming larvae and settled post-larvae of the sponge Amphimedon queenslandica that were exposed to one of three different settlement cues for 2 hours at 1.5, 3, 5 and 8 hours post emergence (hpe).

data_processing:
Raw CEL-Seq reads were processed using a publicly available pipeline (https://github.com/yanailab/CEL-Seq-pipeline).
The demultiplexed reads were mapped to the Amphimedon queenslandica Aqu2.1 gene models (Fernandez-Valverde et al., 2015) and read counts were generated. The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/.
The identifiers in my processed data are searchable in the EnsemblMetazoa database (http://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index). The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/ and are cited in 'Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. Selene L. Fernandez-Valverde, Andrew D. Calcino and Bernard M. Degnan. BMC Genomics 2015, 16:387’.
Supplementary_files_format_and_content: Tab-delimited text file including raw count values for each sample.

organism: Amphimedon queenslandica

source_name: single larva

extract_protocol:
RNA was isolated from individual Amphimedon queenslandica larvae and settled post-larvae using TRIzol as previously described (Jindrich et al., 2017).
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

tag: developmental state

tag: library

value: C

tag: time at induction (hours post emergence; hpe)

tag: age at sequencing (hours post emergence; hpe)

tag: treatment (settlement cue)

value: mesophyllum


title: ind8hpe_mesophyllum_settled_larva_4_46


title: EAE,rep1,Neg,Plate2,B2


title: Str_Glast_KO2_J4 pJ

value: striatum & ventricular-subventricular zone

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


title: EAE,rep1,Neg,Plate2,B6

value: Isolated Microglia


title: EAE,rep1,Neg,Plate2,C2


title: EAE,rep1,Neg,Plate2,B4

value: Adult Spinal Cord Homeostatic


title: Str_Glast_KO2_K1 pJ

value: 2 days post ischemia


title: Str_Glast_KO2_J10 pJ

value: neurogenic striatal astrocyte


title: ind8hpe_mesophyllum_settled_larva_2_44


title: EAE,rep1,Neg,Plate2,B1

value: EAE


title: ind8hpe_mesophyllum_settled_larva_3_45


title: ind8hpe_mesophyllum_settled_larva_6_47


title: EAE,rep1,Neg,Plate2,A8

value: 2 months


title: EAE,rep1,Neg,Plate2,B12


title: Str_Glast_KO2_I8 pJ

value: astrocyte (striatum)


title: ind8hpe_mesophyllum_settled_larva_8_02


title: EAE,rep1,Neg,Plate2,B11


title: EAE,rep1,Neg,Plate2,A7


title: EAE,rep1,Neg,Plate2,B10


title: EAE,rep1,Neg,Plate2,B3


title: Str_Glast_KO2_J1 pJ


title: Str_Glast_KO2_I7 pJ


title: Str_Glast_KO2_I9 pJ


title: ind8hpe_mesophyllum_8_swimming_larva_27


title: EAE,rep1,Neg,Plate2,A4


title: EAE,rep1,Neg,Plate2,A9


title: EAE,rep1,Neg,Plate2,A3


title: Str_Glast_KO2_J3 pJ


title: Str_Glast_KO2_I4 pJ


title: ind8hpe_mesophyllum_9_swimming_larva_28


title: EAE,rep1,Neg,Plate2,A6


title: EAE,rep1,Neg,Plate2,A11

value: Adult Brain Homeostatic


title: Str_Glast_KO2_I5 pJ


title: EAE,rep1,Neg,Plate2,A5

value: Spinal Cord

value: DAM 1


title: ind8hpe_mesophyllum_4_swimming_larva_45

value: T


title: EAE,rep1,Neg,Plate1,H8

value: Neg


title: EAE,rep1,Neg,Plate2,A1

value: IEG+


title: Str_Glast_KO2_I2 pJ


title: EAE,rep1,Neg,Plate2,A2


title: EAE,rep1,Neg,Plate1,H6

value: MHCII+


title: EAE,rep1,Neg,Plate2,A12


title: ind8hpe_mesophyllum_5_swimming_larva_46

value: mesophyllum


title: Str_Glast_KO1_H9 pJ

value: striatum & ventricular-subventricular zone


title: ind8hpe_mesophyllum_10_swimming_larva_29

value: C


title: Str_Glast_KO2_I3 pJ

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


title: EAE,rep1,Neg,Plate2,A10

value: Isolated Microglia


title: EAE,rep1,Neg,Plate1,H3


title: ind8hpe_mesophyllum_6_swimming_larva_25


title: Str_Glast_KO2_I12 pJ

value: 2 days post ischemia


title: ind8hpe_mesophyllum_7_swimming_larva_26


title: ind8hpe_mesophyllum_settled_larva_1_43


title: ind8hpe_mesophyllum_3_swimming_larva_44


title: Str_Glast_KO1_H7 pJ


title: EAE,rep1,Neg,Plate1,H9

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Neg,Plate1,H5

value: EAE


title: Str_Glast_KO1_H3 pJ


title: EAE,rep1,Neg,Plate1,G7

value: 2 months


title: ind8hpe_fsw_9_swimming_larva_23

value: K

value: fsw


title: EAE,rep1,Neg,Plate1,H4

value: Spinal Cord


title: EAE,rep1,Neg,Plate1,G8


title: Str_Glast_KO1_H5 pJ

value: astrocyte (striatum)


title: EAE,rep1,Neg,Plate1,H11


title: ind8hpe_mesophyllum_1_swimming_larva_43

value: T


title: EAE,rep1,Neg,Plate1,H7

value: Neg


title: EAE,rep1,Neg,Plate1,H2


title: Str_Glast_KO1_H11 pJ


title: ind8hpe_fsw_8_swimming_larva_22


title: EAE,rep1,Neg,Plate1,G9

value: IEG+


title: EAE,rep1,Neg,Plate1,G3

value: MHCII+


title: ind8hpe_fsw_5_swimming_larva_20


title: EAE,rep1,Neg,Plate1,G12


title: EAE,rep1,Neg,Plate1,G2


title: ind8hpe_fsw_7_swimming_larva_21


title: EAE,rep1,Neg,Plate1,H10


title: EAE,rep1,Neg,Plate1,G6


title: Str_Glast_KO1_H2 pJ

value: neurogenic striatal astrocyte


title: EAE,rep1,Neg,Plate1,G11


title: Str_Glast_KO1_H8 pJ

value: striatum & ventricular-subventricular zone


title: EAE,rep1,Neg,Plate1,G5


title: ind8hpe_fsw_2_swimming_larva_18


title: ind8hpe_fsw_6_swimming_larva_20


title: EAE,rep1,Neg,Plate1,G4


title: ind8hpe_fsw_10_swimming_larva_24


title: Str_Glast_KO1_H1 pJ

value: reactive astrocyte


title: ind8hpe_fsw_4_swimming_larva_19


title: ind8hpe_fsw_1_swimming_larva_17


title: Str_Glast_KO1_G4 pJ

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


title: Str_Glast_KO1_G3 pJ


title: Str_Glast_KO1_G9 pJ


title: EAE,rep1,Neg,Plate1,F5

value: Isolated Microglia


title: EAE,rep1,Neg,Plate1,G10


title: Str_Glast_KO1_G5 pJ

value: 2 days post ischemia


title: Str_Glast_KO1_G2 pJ


title: EAE,rep1,Neg,Plate1,G1


title: Str_Glast_KO1_G11 pJ


title: EAE,rep1,Neg,Plate1,F8


title: EAE,rep1,Neg,Plate1,F9


title: ind8hpe_amphiroa_settled_larva_5_36

value: C

value: amphiroa


title: EAE,rep1,Neg,Plate1,F11

value: EAE

value: 2 months


title: EAE,rep1,Neg,Plate1,F6

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Neg,Plate1,F10

value: Spinal Cord


title: EAE,rep1,Neg,Plate1,F7


title: ind8hpe_amphiroa_settled_larva_7_38


title: ind8hpe_amphiroa_settled_larva_6_37


title: EAE,rep1,Neg,Plate1,F3


title: EAE,rep1,Neg,Plate1,E8


title: EAE,rep1,Neg,Plate1,F2


title: EAE,rep1,Neg,Plate1,F12


title: Str_Glast_KO1_G10 pJ


title: Str_Glast_KO1_F6 pJ

value: astrocyte (striatum)


title: ind8hpe_amphiroa_settled_larva_1_32


title: ind8hpe_amphiroa_settled_larva_3_34


title: ind8hpe_amphiroa_settled_larva_4_35


title: Str_Glast_KO1_F8 pJ


title: EAE,rep1,Neg,Plate1,F4


title: EAE,rep1,Neg,Plate1,E3


title: Str_Glast_KO1_F5 pJ


title: Str_Glast_KO1_F4 pJ


title: EAE,rep1,Neg,Plate1,E5


title: EAE,rep1,Neg,Plate1,E4


title: ind8hpe_amphiroa_settled_larva_2_33


title: Str_Glast_KO1_G1 pJ


title: EAE,rep1,Neg,Plate1,E10


title: ind8hpe_amphiroa_7_swimming_larva_39

value: K


title: EAE,rep1,Neg,Plate1,E2

value: DAM 2

value: Neg


title: EAE,rep1,Neg,Plate1,E12


title: Str_Glast_KO1_F12 pJ


title: EAE,rep1,Neg,Plate1,E11


title: EAE,rep1,Neg,Plate1,E9


title: EAE,rep1,Neg,Plate1,F1

value: MHCII+


title: ind8hpe_amphiroa_6_swimming_larva_38


title: EAE,rep1,Neg,Plate1,D5

value: IEG+


title: EAE,rep1,Neg,Plate1,E1


title: ind8hpe_amphiroa_3_swimming_larva_31

value: T


title: EAE,rep1,Neg,Plate1,D4

value: Early Postnatal Homeostatic


title: EAE,rep1,Neg,Plate1,D3


title: EAE,rep1,Neg,Plate1,E6


title: Str_Glast_KO1_F10 pJ

value: striatum & ventricular-subventricular zone

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


title: ind8hpe_amphiroa_5_swimming_larva_33


title: ind8hpe_amphiroa_4_swimming_larva_32


title: EAE,rep1,Neg,Plate1,D9

value: Isolated Microglia


title: EAE,rep1,Neg,Plate1,D7


title: EAE,rep1,Neg,Plate1,D11


title: Str_Glast_KO1_E5 pJ

value: neurogenic striatal astrocyte

value: 2 days post ischemia


title: EAE,rep1,Neg,Plate1,D10

value: EAE


title: ind8hpe_amphiroa_12_swimming_larva_03

value: C

value: amphiroa


title: ind8hpe_amphiroa_13_swimming_larva_04


title: EAE,rep1,Neg,Plate1,D1

value: Spinal Cord

value: 2 months


title: EAE,rep1,Neg,Plate1,D8


title: Str_Glast_KO1_F11 pJ

value: astrocyte (striatum)


title: Str_Glast_KO1_E7 pJ


title: EAE,rep1,Neg,Plate1,D12

value: Adult Brain Homeostatic


title: ind8hpe_amphiroa_10_swimming_larva_40

value: K


title: ind8hpe_amphiroa_15_swimming_larva_11


title: EAE,rep1,Neg,Plate1,D6

value: Neg


title: EAE,rep1,Neg,Plate1,C9

value: MHCII+


title: Str_Glast_KO1_F1 pJ


title: Str_Glast_KO1_E3 pJ


title: EAE,rep1,Neg,Plate1,D2


title: EAE,rep1,Neg,Plate1,C5

value: Adult Spinal Cord Homeostatic


title: EAE,rep1,Neg,Plate1,C7


title: Str_Glast_KO1_E2 pJ


title: EAE,rep1,Neg,Plate1,C6


title: ind5hpe_mesophyllum_settled_larva_7_40

value: mesophyllum


title: EAE,rep1,Neg,Plate1,C3


title: Str_Glast_KO1_E11 pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_KO1_E1 pJ

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


title: EAE,rep1,Neg,Plate1,C4

value: Isolated Microglia


title: EAE,rep1,Neg,Plate1,C2

value: IEG+


title: EAE,rep1,Neg,Plate1,C12


title: ind5hpe_mesophyllum_settled_larva_6_39


title: EAE,rep1,Neg,Plate1,C11


title: Str_Glast_KO1_D7 pJ

value: neurogenic striatal astrocyte

value: 2 days post ischemia


title: ind5hpe_mesophyllum_settled_larva_5_01

value: C


title: EAE,rep1,Neg,Plate1,C10

value: EAE


title: Str_Glast_KO1_D6 pJ


title: EAE,rep1,Neg,Plate1,C8

value: Spinal Cord


title: EAE,rep1,Neg,Plate1,C1

value: 2 months


title: ind5hpe_mesophyllum_settled_larva_4_48

value: T


title: EAE,rep1,Neg,Plate1,B8


title: ind5hpe_mesophyllum_settled_larva_9_41


title: Str_Glast_KO1_D2 pJ


title: Str_Glast_KO1_D5 pJ


title: ind5hpe_mesophyllum_settled_larva_10_42


title: Str_Glast_KO1_F2 pJ


title: EAE,rep1,Neg,Plate1,B7


title: EAE,rep1,Neg,Plate1,B6


title: ind5hpe_mesophyllum_8_swimming_larva_22


title: ind5hpe_mesophyllum_settled_larva_3_47


title: EAE,rep1,Neg,Plate1,B3


title: EAE,rep1,Neg,Plate1,B2

value: Adult Brain Homeostatic


title: ind5hpe_mesophyllum_9_swimming_larva_23


title: EAE,rep1,Neg,Plate1,B4


title: EAE,rep1,Neg,Plate1,B12


title: Str_Glast_KO1_D1 pJ

value: astrocyte (striatum)


title: Str_Glast_KO1_C9 pJ


title: EAE,rep1,Neg,Plate1,B10

value: Neg


title: EAE,rep1,Neg,Plate1,B9


title: Str_Glast_KO1_C8 pJ


title: EAE,rep1,Neg,Plate1,B11

value: MHCII+


title: ind5hpe_mesophyllum_6_swimming_larva_20


title: EAE,rep1,Neg,Plate1,A9

value: Adult Spinal Cord Homeostatic


title: Str_Glast_KO1_D10 pJ


title: EAE,rep1,Neg,Plate1,B5


title: EAE,rep1,Neg,Plate1,A8


title: ind5hpe_mesophyllum_4_swimming_larva_41

value: mesophyllum


title: Fbn6_S16

city: Los Angeles

first: Sandra

last: Orsulic

state: CA

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

data_processing:
Sequencing was performed on Illumina HiSeq 3000 for SE 1x50 run
Data quality check was done on Illumina SAV
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
The Partek flow software version7.0 was used for the data analysis
The alignment was performed using STAR with mouse reference genome mm10
For normalization of transcripts counts, the normalization method, adding 1.0E-4 followed by counts per million (TMM).  CPM normalized counts were also generated by adding 1.0E-4 followed by counts per million (CPM) normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Tab-delimited text files include TMM values for each sample

source_name: Dorsal skin

extract_protocol:
Six-week old mice were used to isolate mouse skin for RNA extraction for subsequent RNA-Seq.  Upon sacrifice, the dorsal skin was shaved, the mice immediately placed on ice and a rectangular piece of skin was surgically removed using ice-cold micro-dissecting scissors and forceps. The skin was divided into 4 strips of 3-5mm each, immediately snap frozen in liquid nitrogen and stored at -80C until further processing. All mouse skin isolation was performed within 60-70 seconds of sacrifice to prevent RNA degradation. Samples were cut and placed in lysis bead tubes containing RLT buffer supplemented with DTT. The samples were homogenized using the Magna Lyser and RNA was harvested using the RNeasy Mini kit (Qiagen). KAPA Stranded RNA-Seq Kit with RiboErase Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit with RiboErase Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentaion. First strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand.  cDNA generation is followed by A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

tag: strain

value: day 40


title: Str_Glast_KO1_C7 pJ

value: striatum & ventricular-subventricular zone

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


title: ind5hpe_mesophyllum_3_swimming_larva_40


title: EAE,rep1,Neg,Plate1,A7

value: Isolated Microglia


title: Str_Glast_KO1_C5 pJ


title: EAE,rep1,Neg,Plate1,A6


title: Fbn5_S15


title: ind5hpe_mesophyllum_7_swimming_larva_21


title: Str_Glast_KO1_C3 pJ


title: ind5hpe_mesophyllum_11_swimming_larva_07


title: EAE,rep1,Neg,Plate1,A5


title: WT3_S13

value: wild type


title: Str_Glast_KO1_C12 pJ

value: 2 days post ischemia


title: Fbn4_S14


title: ind5hpe_mesophyllum_5_swimming_larva_42


title: Str_Glast_KO1_C2 pJ


title: ind5hpe_mesophyllum_10_swimming_larva_24

value: C


title: EAE,rep1,Neg,Plate1,B1

value: IEG+

value: EAE


title: ind5hpe_fsw_9_swimming_larva_18

value: K

value: fsw


title: Str_Glast_KO1_C11 pJ


title: EAE,rep1,Neg,Plate1,A3

value: Spinal Cord

value: 2 months


title: EAE,rep1,Neg,Plate1,A4

value: Neg


title: ind5hpe_fsw_8_swimming_larva_17


title: WT2_S12


title: ISRIB-3; L444P_24h_ISRIB(biol. rep 3)

city: La Jolla

first: Jeffery

last: Kelly

state: California

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Alignment of reads was performed using DNAstar Lasergene SeqMan NGen 17 to the human genome GRCh38-dbSNP150 assembly.
Aligned reads were imported into ArrayStar 17 as linear counts data.
Differential expression analysis and statistical significance comparisons were assessed using DESeq2 (v. 1.40.1) in R compared to DMSO-treated cells.
Assembly: human genome GRCh38-dbSNP150 assembly
Supplementary files format and content: Raw counts of sequencing reads for each gene following alignment. Format is .csv.
Supplementary files format and content: Normalized abundance measurements for each gene following DESeq2. Format is .csv.

organism: Homo sapiens

source_name: GM08760, Coriell

growth_protocol: Gaucher Fibroblasts (GM08760, Coriell) plated at 300,000 cells/well in a 6-well plate in DMEM with 10% FBS and 1% PennStrep

extract_protocol:
Cells were collected with TryplE (ThermoFisher), neutralized with cell culture media, and pelleted at 1000 x g for 5 min. Total RNA was extracted using the Direct-zol (Zymo Research), following the protocol suggested by the manufacturer.
Libraries were constructed by BGI using their standard methodology. mRNA was enriched from total RNA samples via their polyA tails using oligo dT beads. mRNA was then fragmented and converted to cDNA using random primers to synthesize the first cDNA strand. The second cDNA strand was synthesized using dUTP instead of dTTP. The cDNA was subjected to end-repair and 3’ adenylated. Adaptors were ligated to the ends of these cDNA fragments. The U-labeled second-strand template was digested with uracil-DNA-glycosylase. The remaining cDNA fragments were then amplified by PCR. The library was quality controlled, then circularized and amplified to make a DNA nanoball (DNB). Finally, the library was sequenced using the DNBSEQ platform.

treatment_protocol: After attachment overnight, the cells were treated with the indicated concentration of compound for 24 h.

value: GM08760, Coriell

value: fibroblast

tag: time

value: 24 hour

value: ISRIB (200 nM)


title: Str_Glast_KO1_B9 pJ

value: striatum & ventricular-subventricular zone

value: neurogenic striatal astrocyte


title: WT1_S11

value: day 40


title: ind5hpe_fsw_7_swimming_larva_16


title: EAE,rep1,Neg,Plate1,A2

value: Isolated Microglia

value: MHCII+


title: EAE,rep1,Neg,Plate1,A12


title: ISRIB-2; L444P_24h_ISRIB(biol. rep 2)


title: ind5hpe_fsw_6_swimming_larva_15


title: EAE,rep1,Neg,Plate1,A11


title: Str_Glast_KO1_B8 pJ

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

value: 2 days post ischemia


title: ind5hpe_fsw_5_swimming_larva_16

value: T


title: Str_Glast_KO1_C10 pJ

value: astrocyte (striatum)


title: ISRIB-1; L444P_24h_ISRIB(biol. rep 1)


title: EAE,rep1,Neg,Plate1,A10

value: IEG+

value: EAE


title: ind5hpe_fsw_4_swimming_larva_15

value: fsw


title: Str_Glast_KO1_B3 pJ


title: Apil-3; L444P_24h_Apil(biol. rep 3)

value: Apilimod (50 nM)


title: ind5hpe_fsw_2_swimming_larva_14


title: ind5hpe_fsw_11_swimming_larva_05

value: C


title: Input, mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 1

first: Yi

last: Wang

address: 320 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
To investigate genome-wide H3K9me3 and H3K27me3 histone modifications in cardiomyocytes, we mapped sequencing reads to the mouse genome mm10, using aligner Bowtie 2. Only uniquely mapped reads with no more than 2 mismatches were used for binding peak detection. We employed MACS2 (model-based analysis of ChIP-seq) with broad peak calling arguments at a false discovery rate of less than 0.05 to call peaks.
Assembly: mm10
Supplementary files format and content: bigWig file for each sample

source_name: cardiomyocytes

extract_protocol:
Briefly, ~2 million cardiomyocytes were crosslinked with 1% formaldehyde for 15 minutes at room temperature. Then, the chromatin was fragmented using a QSonica Q800R3 sonicator to obtain an average chromatin length of 300 nucleotides. The fragmented chromatin was incubated with H3K27me3 (CST, #9733) or H3K9me3 antibody (CST, #13969) at 4 °C overnight. The antibody-bound chromatin was immunoprecipitated using protein A/G agarose beads (Thermo Fisher Scientific, #20421).
ChIP-seq library preparation and NGS sequencing were carried out by Novogene Corporation Inc., with at least 50 million tags sequenced for each library using 150 bp pair-ended sequencing.

value: cardiomyocytes

value: GapmeR lincRNA-p21

value: PE


title: Str_Glast_KO1_B12 pJ

value: striatum & ventricular-subventricular zone


title: Apil-2; L444P_24h_Apil(biol. rep 2)

value: GM08760, Coriell

value: fibroblast

value: 24 hour


title: Str_Glast_KO1_B10 pJ


title: ind5hpe_fsw_10_swimming_larva_19

value: K


title: Apil-1; L444P_24h_Apil(biol. rep 1)


title: EAE,rep1,Neg,Plate1,A1

value: Spinal Cord

value: Isolated Microglia

value: 2 months

value: Neg


title: A18-3; L444P_24h_A18(biol. rep 3)


title: Input, mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 1

value: GapmeR negative control

value: PBS


title: Input, mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 1


title: ind5hpe_amphiroa_settled_larva_7_12

value: amphiroa


title: A18-1; L444P_24h_A18(biol. rep 1)


title: ind5hpe_amphiroa_settled_larva_8_15


title: Str_Glast_KO1_B5 pJ

value: astrocyte (striatum)

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

value: 2 days post ischemia


title: Str_Glast_KO1_A8 pJ

value: neurogenic striatal astrocyte


title: Input, mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 1

value: cardiomyocytes

value: GapmeR lincRNA-p21


title: Str_Glast_KO1_A7 pJ

value: striatum & ventricular-subventricular zone


title: Str_Glast_KO1_A6 pJ


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 2

value: PE


title: A16-3; L444P_24h_A16(biol. rep 3)

value: GM08760, Coriell

value: fibroblast

value: 24 hour


title: A18-2; L444P_24h_A18(biol. rep 2)


title: A16-2; L444P_24h_A16(biol. rep 2)


title: Str_Glast_KO1_A5 pJ


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 1


title: ind5hpe_amphiroa_settled_larva_5_09

value: C


title: Str_Glast_KO1_A9 pJ


title: DMSO-3; L444P_24h_DMSO(biol. rep 3)

value: DMSO


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 2


title: A16-1; L444P_24h_A16(biol. rep 1)


title: Str_Glast_KO1_A4 pJ


title: Str_Glast_KO1_A12 pJ


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 1


title: ind5hpe_amphiroa_settled_larva_1_30


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 2


title: DMSO-2; L444P_24h_DMSO(biol. rep 2)


title: Str_Glast_KO1_A10 pJ


title: ind5hpe_amphiroa_8_swimming_larva_35

value: K


title: DMSO-1; L444P_24h_DMSO(biol. rep 1)


title: ind5hpe_amphiroa_settled_larva_6_10


title: Str_Glast_KO1_A1 pJ


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 2

value: GapmeR negative control


title: ind5hpe_amphiroa_7_swimming_larva_34


title: E. cloacae wild-type, 15°C, replicate E

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts. Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Reads were aligned to the reference genomes using BWA v0.7.17 . Reads were counted with htseq-count v2.0.1
Assembly: 6 species are present here, so there are six reference sequences: GCF_000005845.2,GCF_000022165.1,GCF_000027085.1,GCF_000281535.2,GCF_000025565.1,GCF_000513215.1
Supplementary files format and content: Processed files are text files of (unnormalized) counts for each sample.

organism: Enterobacter cloacae

growth_protocol: Bacteria were grown in LB at 37°C

extract_protocol:
1.5 mL of bacterial culture was pelleted and resuspended in 500 μL of Trizol pre-heated to 65°C and then stored at -80°C until use. Samples were purified on a column using the Zymo Direct-Zol RNA Miniprep kit. They were then treated twice with DNase I using Turbo DNA-free (Invitrogen) for 30 minutes each at 37˚C to ensure that all DNA was degraded. The samples were further purified on a column using the Zymo RNA Clean and Concentrator Kit and again stored at -80˚C until sequencing.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol. Briefly, 500 ng to 1 μg of total RNA was fragmented by heating to 94°C in NEB Alkaline Phosphatase Buffer, depleted of any residual genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described (23); (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform at the Broad Institute to generate paired end reads.

treatment_protocol: At time 0, samples were taken and cultures shifted to 15°C. Cells grew at 15°C for 3 hours, and then sampleres were taken again

value: wild-type

tag: biological replicate

value: E


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 1

value: PBS


title: E. cloacae wild-type, 37°C, replicate E


title: ind5hpe_amphiroa_6_swimming_larva_33

value: amphiroa


title: ind5hpe_amphiroa_settled_larva_4_31


title: ind5hpe_amphiroa_5_swimming_larva_30

value: T


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 1


title: E. cloacae wild-type, 15°C, replicate D

value: D


title: ind5hpe_amphiroa_9_swimming_larva_36


title: ind5hpe_amphiroa_4_swimming_larva_29


title: E. cloacae wild-type, 37°C, replicate D


title: E. cloacae wild-type, 15°C, replicate B

value: B


title: ind5hpe_amphiroa_3_swimming_larva_28


title: Liver_ko_3

first: Joana

middle: A

last: Vidigal

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 96%
Assembly: mm10
Supplementary files format and content: count table

source_name: Liver

extract_protocol:
RNA from brains and livers from Vaultrc5+/+ and Vaultrc5-/- mice was isolated using TRIzol reagent (Invitrogen) following the manufacturers’ protocol. RNA was then treated with DNase I using Zymo RNA clean & concentrator kit
12 totalRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and single-end sequencing
Stranded Total RNA Prep

tag: tissue

value: Liver

tag: Sex

value: male


title: Liver_ko_1


title: Liver_flx_2


title: Liver_flx_3


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 2

tag: cell type

value: cardiomyocytes

value: PE


title: ind5hpe_amphiroa_10_swimming_larva_37


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 1


title: H3K27me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 1

value: GapmeR lincRNA-p21


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 2


title: Liver_ko_2


title: Liver_flx_1


title: E. cloacae wild-type, 37°C, replicate B


title: Brain_ko_3

value: Brain


title: E. cloacae wild-type, 15°C, replicate A

value: A


title: Brain_ko_2


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 2


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 1


title: ind3hpe_mesophyllum_8_swimming_larva_48

value: mesophyllum


title: E. cloacae wild-type, 37°C, replicate A


title: ind5hpe_amphiroa_1_swimming_larva_27


title: MCF7 cells, -SerGly 48 hr, rep 3

city: Chicago

first: Svetlana

last: Semina

address: 909 S Wolcott Avenue (MC 901), 2100 COMRB

department: physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: NCBI/UCSC/Ensembl
Supplementary files format and content: NA

growth_protocol: MCF7 cells were maintained in HPLM with 5% dFBS and pen/strep in a humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X) or by using sonication with Diagenode bioruptor Pico for breaking RNA strands. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: MCF7 cells were treated with and without serine and glycine for 48 hours.

tag: cell line

value: breast cancer

value: Minus Ser/Gly 48 hr


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 2


title: Brain_ko_1

tag: age


title: H3K9me3 ChIP-seq, mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 1

value: GapmeR negative control


title: ind3hpe_mesophyllum_7_swimming_larva_47

value: K


title: Brain_flx_3

value: wild-type


title: MCF7 cells, -SerGly 48 hr, rep 2


title: MCF7 cells, -SerGly 48 hr, rep 1


title: ind3hpe_mesophyllum_6_swimming_larva_46