title: EKHT4_ROW11_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 80


title: EKHT4_ROW10_5: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 73

status: Public on Jul 01 2021

type: SRA

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

library_source: transcriptomic

data_processing:
bulk RNA-seq reads were parsed to extract: sindbis barcode (nucleotide 1-32), sinbis index (nuceodite 89-94), and umi sequence (nucleotide 95-106).
RNA-seq reads are deduplicated on the base of the UMI sequence
RNA-seq reads are tagged as viral, spike or unknown depending on their barcode sequence
Single-cell gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Barcodes found in the single cell of the injection site are clustered to correct for sequencing errors
Barcodes from the target regions are mapped to the error-corrected barcodes found in the injection sites
Counts are normalized with the number of spike found in the same target region
Genome_build: Single cell reads are mapped to mm10 genome (no mapping for bulk reads because it is a barcode sequencing protocol)
Supplementary_files_format_and_content: connectID_links.tsv.gz contains the result of the parsing of the sindbis reads. The file report the amount of unique umi sequence of a target that was associated to a barcode of the injection site. It also report include the number of spike in the region and te number of time the barcode was seen in the injection site.
Supplementary_files_format_and_content: connectID_S1_cells_metadata.tsv.gz contains meta-data for each single-cell, together with connection information extracted from the barcodes
Supplementary_files_format_and_content: connectID_S1_cells_count_matrix.tsv.gz contains the gene expression count matrix of every single cell

molecule: polyA RNA

organism: Mus musculus

source_name: cortex S1

extract_protocol:
The primary somatosensory cortex was microdissected as aforementioned. Cells were further dissociated by incubating micro-dissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by incubation in 5% bovine serum albumin for 3 minutes and manual trituration in ACSF using pulled glass pipettes. Cells were then centrifuged for 10 minutes at 600 rpm and resuspended before filtration using a 70 mm cell strainer (ClearLine, # 141379C). Cells were then incubated for 10 minutes at 37°C with Hoechst (0.1 mg/mL) and isolated using a Beckman Coulter Moflo Astrios FAC-sorter. Singlet Hoechst+cells were sorted according to their Forward and Side scattering properties (FSC and SSC), and their negativity for Draq7TM (Viability dye, Far red DNA intercalating agent, Beckman Coulter, #B25595). 5000 to 10 000 cells were FACsorted for each experiment. Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ml of FAC-sorted cells GFP+ cells, yielding a 300-500 cells / ml suspension. 12 ml of this suspension mix were loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 mm diameter-cells (Fluidigm, #100-5780). RNA was extracted using an RNeasy kit (Qiagen, #74034), and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.
SMARTseq v4 kit (Clontech, # 634888)

tag: strain

tag: tissue

value: cortex S1

tag: dissection


title: EKHT4_ROW11_18: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 76


title: EKHT4_ROW16_18: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 116


title: EKHT4_ROW11_12: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 74


title: EKHT4_ROW10_19: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 71


title: EKHT4_ROW11_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 75


title: EKHT4_ROW10_18: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 70


title: EKHT4_ROW12_6: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 89


title: EKHT4_ROW12_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 86


title: EKHT4_ROW15_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 107


title: EKHT4_ROW10_11: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 66


title: EKHT4_ROW10_14: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 68


title: EKHT4_ROW09_9: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 65


title: EKHT4_ROW09_6: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 63


title: EKHT4_ROW10_13: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 67


title: EKHT4_ROW09_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 64


title: EKHT4_ROW09_14: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 57


title: EKHT4_ROW10_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 72


title: EKHT4_ROW09_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 58


title: EKHT4_ROW08_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 53


title: EKHT4_ROW09_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 61


title: EKHT4_ROW10_16: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 69


title: EKHT4_ROW09_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 62


title: EKHT4_ROW11_6: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 79


title: EKHT4_ROW09_13: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 56


title: EKHT4_ROW08_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 50


title: EKHT4_ROW08_16: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 51


title: EKHT4_ROW09_10: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 55


title: EKHT4_ROW08_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 54


title: EKHT4_ROW07_3: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 45


title: EKHT4_ROW07_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 47


title: EKHT4_ROW08_14: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 49


title: EKHT4_ROW07_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 46


title: EKHT4_ROW08_13: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 48


title: EKHT4_ROW07_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 44


title: EKHT4_ROW06_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 40


title: EKHT4_ROW06_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 36


title: EKHT4_ROW06_16: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 37


title: EKHT4_ROW06_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 42


title: EKHT4_ROW09_2: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 60


title: EKHT4_ROW05_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 33


title: EKHT4_ROW05_18: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 31


title: EKHT4_ROW08_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 52


title: EKHT4_ROW09_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 59


title: EKHT4_ROW06_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 39


title: EKHT4_ROW07_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 43


title: EKHT4_ROW06_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 38


title: EKHT4_ROW05_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 30


title: EKHT4_ROW04_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 29


title: EKHT4_ROW04_5: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 27


title: EKHT4_ROW06_6: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 41


title: EKHT4_ROW06_12: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 35


title: EKHT4_ROW05_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 34


title: EKHT4_ROW04_13: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 19


title: EKHT4_ROW04_7: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 28


title: EKHT4_ROW04_3: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 25


title: EKHT4_ROW05_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 32


title: EKHT4_ROW03_12: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 14


title: EKHT4_ROW04_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 26


title: EKHT4_ROW02_4: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 10


title: EKHT4_ROW01_9: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 8


title: EKHT4_ROW04_19: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 23


title: EKHT4_ROW04_20: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 24


title: EKHT4_ROW02_3: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 9


title: EKHT4_ROW04_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 22


title: EKHT4_ROW01_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 4


title: EKHT4_ROW04_14: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 20


title: EKHT4_ROW04_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 21


title: EKHT4_ROW01_12: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 2


title: EKHT4_ROW01_10: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 1


title: EKHT4_ROW03_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 18


title: EKHT4_ROW03_17: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 16


title: EKHT3_ROW40_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 134


title: EKHT3_ROW39_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 132


title: EKHT4_ROW03_16: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 15


title: EKHT4_ROW02_8: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 12


title: EKHT3_ROW37_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 127


title: EKHT4_ROW01_2: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 7


title: EKHT4_ROW01_19: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 6


title: EKHT4_ROW03_10: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 13


title: EKHT3_ROW36_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 122


title: EKHT4_ROW01_18: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 5


title: EKHT3_ROW35_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 120


title: EKHT3_ROW34_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 118


title: EKHT4_ROW03_2: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 17


title: EKHT3_ROW40_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 135


title: EKHT4_ROW01_15: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 3


title: EKHT3_ROW39_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 133


title: EKHT3_ROW33_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 116


title: EKHT3_ROW33_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 114


title: EKHT4_ROW02_7: Reads from single cell RNA-seq of the S1 injection site of either pup A1, cell 11


title: EKHT3_ROW31_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 111


title: EKHT3_ROW30_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 110


title: EKHT3_ROW29_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 107


title: EKHT3_ROW38_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 130


title: EKHT3_ROW38_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 129


title: EKHT3_ROW37_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 126


title: EKHT3_ROW36_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 125


title: EKHT3_ROW36_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 123


title: EKHT3_ROW27_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 102


title: EKHT3_ROW35_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 121


title: EKHT3_ROW40_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 136


title: EKHT3_ROW34_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 119


title: EKHT3_ROW39_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 131


title: EKHT3_ROW33_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 117


title: EKHT3_ROW25_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 95


title: EKHT3_ROW24_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 93


title: EKHT3_ROW33_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 115


title: EKHT3_ROW24_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 91


title: EKHT3_ROW37_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 128


title: EKHT3_ROW36_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 124


title: EKHT3_ROW33_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 113


title: EKHT3_ROW32_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 112


title: EKHT3_ROW30_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 109


title: EKHT3_ROW30_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 108


title: EKHT3_ROW29_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 106


title: EKHT3_ROW28_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 104


title: EKHT3_ROW29_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 105


title: EKHT3_ROW26_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 98


title: EKHT3_ROW28_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 103


title: EKHT3_ROW26_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 97


title: EKHT3_ROW27_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 99


title: EKHT3_ROW21_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 83


title: EKHT3_ROW20_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 79


title: EKHT3_ROW25_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 94


title: EKHT3_ROW21_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 81


title: EKHT3_ROW27_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 100


title: EKHT3_ROW24_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 92


title: EKHT3_ROW20_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 76


title: EKHT3_ROW27_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 101


title: EKHT3_ROW19_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 74


title: EKHT3_ROW24_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 90


title: EKHT3_ROW23_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 89


title: EKHT3_ROW26_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 96


title: EKHT3_ROW23_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 88


title: EKHT3_ROW23_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 87


title: EKHT3_ROW22_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 86


title: EKHT3_ROW22_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 85


title: EKHT3_ROW19_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 73


title: EKHT3_ROW18_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 72


title: EKHT3_ROW22_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 84


title: EKHT3_ROW21_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 82


title: EKHT3_ROW20_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 78


title: EKHT3_ROW19_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 75


title: EKHT3_ROW20_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 77


title: EKHT3_ROW18_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 71


title: EKHT3_ROW18_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 70


title: EKHT3_ROW18_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 68


title: EKHT3_ROW17_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 67


title: EKHT3_ROW17_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 66


title: EKHT3_ROW17_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 65


title: EKHT3_ROW20_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 80


title: EKHT3_ROW17_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 64


title: EKHT3_ROW17_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 63


title: EKHT3_ROW13_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 49


title: EKHT3_ROW18_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 69


title: EKHT3_ROW11_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 45


title: EKHT3_ROW09_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 40


title: EKHT3_ROW17_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 62


title: EKHT3_ROW16_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 61


title: EKHT3_ROW15_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 60


title: EKHT3_ROW15_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 59


title: EKHT3_ROW08_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 36


title: EKHT3_ROW15_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 58


title: EKHT3_ROW14_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 57


title: EKHT3_ROW08_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 34


title: EKHT3_ROW14_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 54


title: EKHT3_ROW07_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 33


title: EKHT3_ROW14_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 53


title: EKHT3_ROW07_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 32


title: EKHT3_ROW14_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 52


title: EKHT3_ROW13_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 51


title: EKHT3_ROW13_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 50


title: EKHT3_ROW09_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 37


title: EKHT3_ROW12_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 48


title: EKHT3_ROW09_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 39


title: EKHT3_ROW12_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 47


title: EKHT3_ROW10_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 44


title: EKHT3_ROW14_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 56


title: EKHT3_ROW07_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 29


title: EKHT3_ROW11_19: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 46


title: EKHT3_ROW07_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 30


title: EKHT3_ROW10_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 43


title: EKHT3_ROW06_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 28


title: EKHT3_ROW09_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 38


title: EKHT3_ROW08_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 35


title: EKHT3_ROW14_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 55


title: EKHT3_ROW10_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 42


title: EKHT3_ROW06_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 24


title: EKHT3_ROW06_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 23


title: EKHT3_ROW05_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 22


title: EKHT3_ROW05_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 20


title: EKHT3_ROW04_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 17


title: EKHT3_ROW05_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 18


title: EKHT3_ROW06_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 27


title: EKHT3_ROW04_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 15


title: EKHT3_ROW06_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 25


title: EKHT3_ROW03_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 13


title: EKHT3_ROW06_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 26


title: EKHT3_ROW05_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 21


title: EKHT3_ROW07_15: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 31


title: EKHT3_ROW03_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 10


title: EKHT3_ROW05_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 19


title: EKHT3_ROW04_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 16


title: EKHT3_ROW01_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 4


title: EKHT3_ROW03_20: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 14


title: EKHT3_ROW01_11: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 1


title: EKHT3_ROW10_12: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 41


title: 20_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 163


title: EKHT3_ROW03_16: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 12


title: 20_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 160


title: EKHT3_ROW02_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 9


title: EKHT3_ROW03_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 11


title: 20_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 159


title: EKHT3_ROW02_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 8


title: EKHT3_ROW01_18: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 6


title: 20_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 157


title: EKHT3_ROW01_17: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 5


title: 20_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 158


title: EKHT3_ROW01_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 3


title: 20_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 154


title: EKHT3_ROW01_13: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 2


title: 19_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 150


title: 20_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 156


title: 20_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 162


title: 20_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 155


title: EKHT3_ROW02_14: Reads from single cell RNA-seq of the S1 injection site of either pup Z2, cell 7


title: 20_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 153


title: 20_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 151


title: 19_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 147


title: 19_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 149


title: 19_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 146


title: 20_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 161


title: 19_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 140


title: 19_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 138


title: 19_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 139


title: 19_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 145


title: 19_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 141


title: 19_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 136


title: 19_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 137


title: 20_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 152


title: 18_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 135


title: 18_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 134


title: 18_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 130


title: 19_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 142


title: 18_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 131


title: 18_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 129


title: 18_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 126


title: 18_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 125


title: 19_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 144


title: 18_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 122


title: 18_ROW21_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 128


title: 18_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 133


title: 17_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 114


title: 19_ROW21_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 143


title: 18_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 127


title: 17_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 113


title: 18_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 123


title: 17_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 111


title: 18_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 124


title: 17_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 110


title: 18_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 121


title: 18_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 119


title: 17_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 117


title: 17_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 116


title: 18_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 132


title: 17_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 107


title: 18_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 120


title: 17_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 108


title: 17_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 115


title: 16_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 104


title: 16_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 105


title: 18_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 118


title: 16_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 102


title: 17_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 109


title: 16_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 106


title: 17_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 112


title: 16_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 99


title: 16_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 98


title: 16_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 95


title: 16_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 101


title: 16_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 103


title: 16_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 96


title: 16_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 97


title: 16_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 94


title: 16_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 100


title: 19_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 148


title: 16_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 93


title: 16_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 92


title: 16_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 90


title: 16_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 91


title: 16_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 89


title: 16_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 88


title: 16_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 87


title: 16_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 86


title: 15_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 81


title: 15_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 82


title: 15_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 80


title: 16_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 85


title: 15_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 83


title: 15_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 79


title: 15_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 78


title: 15_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 76


title: 15_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 75


title: 15_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 73


title: 15_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 74


title: 15_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 71


title: 16_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 84


title: 15_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 70


title: 15_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 68


title: 15_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 69


title: 14_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 65


title: 14_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 66


title: 14_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 67


title: 14_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 64


title: 14_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 62


title: 14_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 63


title: 14_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 61


title: 14_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 60


title: 14_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 59


title: 14_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 58


title: 14_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 54


title: 14_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 52


title: 14_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 53


title: 14_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 51


title: 14_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 57


title: 15_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 77


title: 14_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 56


title: 14_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 55


title: 15_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 72


title: 13_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 50


title: 13_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 46


title: 13_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 47


title: 13_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 44


title: 13_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 42


title: 13_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 49


title: 13_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 48


title: 13_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 40


title: 13_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 35


title: 13_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 45


title: 12_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 30


title: 13_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 31


title: 12_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 27


title: 12_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 25


title: 13_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 41


title: 12_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 23


title: 13_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 43


title: 13_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 36


title: 12_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 22


title: 13_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 39


title: 13_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 38


title: 12_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 18


title: 12_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 17


title: 11_ROW37_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 15


title: 13_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 37


title: 11_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 14


title: 11_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 13


title: 12_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 24


title: 13_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 34


title: 11_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 10


title: 12_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 29


title: 13_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 32


title: 13_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 33


title: 11_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 9


title: 11_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 8


title: 12_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 26


title: 12_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 28


title: 11_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 4


title: 12_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 21


title: 12_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 19


title: 11_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 16


title: 11_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 12


title: 11_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 11


title: 11_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 7


title: 11_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 5


title: 11_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 6


title: 10_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 166


title: 10_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 168


title: 10_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 171


title: 10_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 163


title: 10_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 164


title: 11_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 2


title: 11_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 1


title: 10_ROW33_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 176


title: 10_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 160


title: 10_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 177


title: 10_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 175


title: 9_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 156


title: 9_ROW34_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 155


title: 10_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 174


title: 11_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 3


title: 10_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 173


title: 10_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 172


title: 12_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X3 or X4, cell 20


title: 10_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 170


title: 9_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 149


title: 10_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 169


title: 9_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 148


title: 9_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 150


title: 9_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 145


title: 10_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 167


title: 10_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 162


title: 10_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 165


title: 10_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 161


title: 9_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 140


title: 10_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 158


title: 9_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 141


title: 9_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 154


title: 9_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 151


title: 9_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 152


title: 9_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 147


title: 9_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 139


title: 9_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 146


title: 8_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 136


title: 8_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 133


title: 8_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 134


title: 8_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 132


title: 9_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 143


title: 8_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 131


title: 9_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 144


title: 10_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 159


title: 9_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 157


title: 8_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 129


title: 9_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 142


title: 9_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 153


title: 8_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 137


title: 8_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 138


title: 8_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 127


title: 8_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 126


title: 8_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 123


title: 8_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 135


title: 8_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 130


title: 7_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 120


title: 8_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 125


title: 8_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 124


title: 7_ROW34_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 119


title: 7_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 110


title: 7_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 114


title: 7_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 112


title: 7_ROW23_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 115


title: 8_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 121


title: 7_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 107


title: 7_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 108


title: 7_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 117


title: 7_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 116


title: 7_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 103


title: 7_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 118


title: 7_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 104


title: 7_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 106


title: 6_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 100


title: 6_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 98


title: 8_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 128


title: 7_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 109


title: 7_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 111


title: 6_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 102


title: 7_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 113


title: 6_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 101


title: 8_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 122


title: 7_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 105


title: 6_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 93


title: 6_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 91


title: 6_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 99


title: 6_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 92


title: 6_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 90


title: 6_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 86


title: 6_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 95


title: 6_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 97


title: 5_ROW37_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 83


title: 6_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 89


title: 6_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 94


title: 6_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 85


title: 6_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 88


title: 5_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 81


title: 6_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 87


title: 5_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 78


title: 5_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 75


title: 5_ROW26_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 79


title: 5_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 84


title: 5_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 73


title: 5_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 80


title: 5_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 76


title: 5_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 77


title: 6_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 96


title: 5_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 74


title: 4_ROW40_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 70


title: 4_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 69


title: 5_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 82


title: 4_ROW37_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 68


title: 4_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 63


title: 4_ROW28_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 66


title: 4_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 62


title: 4_ROW08_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 61


title: 4_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 59


title: 5_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 71


title: 3_ROW39_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 58


title: 5_ROW03_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 72


title: 3_ROW37_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 56


title: 4_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 64


title: 3_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 51


title: 3_ROW38_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 57


title: 3_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 55


title: 3_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 54


title: 3_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 53


title: 4_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 67


title: 4_ROW18_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 65


title: 3_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 48


title: 3_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 44


title: 3_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 46


title: 3_ROW21_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 50


title: 3_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 45


title: 3_ROW24_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 52


title: 3_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 49


title: 3_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 47


title: 3_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 43


title: 4_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 60


title: 3_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 42


title: 3_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 39


title: 3_ROW06_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 40


title: 3_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 41


title: 2_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 34


title: 3_ROW04_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 38


title: 2_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 31


title: 2_ROW37_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 37


title: 2_ROW35_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 36


title: 2_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 28


title: 2_ROW34_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 35


title: 2_ROW31_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 33


title: 2_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 32


title: 2_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 29


title: 2_ROW01_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 18


title: 2_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 25


title: 2_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 20


title: 2_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 22


title: 2_ROW15_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 27


title: 2_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 24


title: 1_ROW32_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 16


title: 2_ROW09_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 21


title: 2_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 26


title: 1_ROW25_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 13


title: 2_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 19


title: 2_ROW11_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 23


title: 1_ROW29_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 14


title: 1_ROW22_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 12


title: 1_ROW14_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 7


title: 1_ROW20_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 11


title: 1_ROW16_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 8


title: 1_ROW36_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 17


title: 1_ROW05_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 2


title: 2_ROW27_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 30


title: 1_ROW10_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 4


title: P9_2_S2: Sindbis reads sequenced from dissected target S2 in pup 2 at age P9

molecule: total RNA

source_name: cortex S2

extract_protocol:
Trizol Chloroform RNA extraction
Sindbis specific library preparation

value: cortex S2


title: P9_1_V: Sindbis reads sequenced from dissected target V in pup 1 at age P9

source_name: cortex V

value: cortex V

value: V


title: P9_2_A: Sindbis reads sequenced from dissected target A in pup 2 at age P9

source_name: cortex A

value: cortex A

value: A


title: P9_1_Sub: Sindbis reads sequenced from dissected target Sub in pup 1 at age P9

source_name: cortex Sub

value: cortex Sub

value: Sub


title: P9_2_C: Sindbis reads sequenced from dissected target C in pup 2 at age P9

source_name: cortex C

value: cortex C

value: C


title: 1_ROW13_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 6


title: 1_ROW12_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 5


title: 1_ROW17_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 9


title: P9_1_A: Sindbis reads sequenced from dissected target A in pup 1 at age P9


title: 1_ROW07_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 3


title: 1_ROW02_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 1


title: P7_5_Sub: Sindbis reads sequenced from dissected target Sub in pup 5 at age P7


title: P9_2_Sub: Sindbis reads sequenced from dissected target Sub in pup 2 at age P9


title: P9_2_V: Sindbis reads sequenced from dissected target V in pup 2 at age P9


title: P7_5_A: Sindbis reads sequenced from dissected target A in pup 5 at age P7


title: 1_ROW30_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 15


title: P7_5_C: Sindbis reads sequenced from dissected target C in pup 5 at age P7


title: P14_Z2_S2: Sindbis reads sequenced from dissected target S2 in pup Z2 at age P14


title: 1_ROW19_EKHT2: Reads from single cell RNA-seq of the S1 injection site of either pup X1 or X2, cell 10


title: P9_1_S2: Sindbis reads sequenced from dissected target S2 in pup 1 at age P9


title: P9_2_M: Sindbis reads sequenced from dissected target M in pup 2 at age P9

source_name: cortex M

value: cortex M

value: M


title: P9_1_M: Sindbis reads sequenced from dissected target M in pup 1 at age P9


title: P9_1_C: Sindbis reads sequenced from dissected target C in pup 1 at age P9


title: P14_X4_Sub: Sindbis reads sequenced from dissected target Sub in pup X4 at age P14


title: P7_5_V: Sindbis reads sequenced from dissected target V in pup 5 at age P7


title: P14_X4_C: Sindbis reads sequenced from dissected target C in pup X4 at age P14


title: P14_X4_A: Sindbis reads sequenced from dissected target A in pup X4 at age P14


title: P14_X4_S2: Sindbis reads sequenced from dissected target S2 in pup X4 at age P14


title: P14_Z2_V: Sindbis reads sequenced from dissected target V in pup Z2 at age P14


title: P7_5_M: Sindbis reads sequenced from dissected target M in pup 5 at age P7


title: P14_X3_M: Sindbis reads sequenced from dissected target M in pup X3 at age P14


title: P14_Z2_M: Sindbis reads sequenced from dissected target M in pup Z2 at age P14


title: P14_Z2_C: Sindbis reads sequenced from dissected target C in pup Z2 at age P14


title: P14_Z2_A: Sindbis reads sequenced from dissected target A in pup Z2 at age P14


title: P14_X3_A: Sindbis reads sequenced from dissected target A in pup X3 at age P14


title: P14_X2_Sub: Sindbis reads sequenced from dissected target Sub in pup X2 at age P14


title: P14_X4_M: Sindbis reads sequenced from dissected target M in pup X4 at age P14


title: P14_X2_C: Sindbis reads sequenced from dissected target C in pup X2 at age P14


title: P14_X3_Sub: Sindbis reads sequenced from dissected target Sub in pup X3 at age P14


title: P14_X3_V: Sindbis reads sequenced from dissected target V in pup X3 at age P14


title: P7_5_S2: Sindbis reads sequenced from dissected target S2 in pup 5 at age P7


title: P14_X3_S2: Sindbis reads sequenced from dissected target S2 in pup X3 at age P14


title: P14_X1_M: Sindbis reads sequenced from dissected target M in pup X1 at age P14


title: P14_X1_S2: Sindbis reads sequenced from dissected target S2 in pup X1 at age P14


title: P14_B1_V: Sindbis reads sequenced from dissected target V in pup B1 at age P14


title: P14_B1_S2: Sindbis reads sequenced from dissected target S2 in pup B1 at age P14


title: P14_X2_V: Sindbis reads sequenced from dissected target V in pup X2 at age P14


title: P14_X2_S2: Sindbis reads sequenced from dissected target S2 in pup X2 at age P14


title: P14_X2_M: Sindbis reads sequenced from dissected target M in pup X2 at age P14


title: P14_Z2_Sub: Sindbis reads sequenced from dissected target Sub in pup Z2 at age P14


title: P14_X4_V: Sindbis reads sequenced from dissected target V in pup X4 at age P14


title: P14_A1_S2: Sindbis reads sequenced from dissected target S2 in pup A1 at age P14


title: P14_A1_C: Sindbis reads sequenced from dissected target C in pup A1 at age P14


title: P14_3_V: Sindbis reads sequenced from dissected target V in pup 3 at age P14


title: P14_3_Sub: Sindbis reads sequenced from dissected target Sub in pup 3 at age P14


title: P14_X3_C: Sindbis reads sequenced from dissected target C in pup X3 at age P14


title: P14_X1_V: Sindbis reads sequenced from dissected target V in pup X1 at age P14


title: P14_3_S2: Sindbis reads sequenced from dissected target S2 in pup 3 at age P14


title: P14_X1_C: Sindbis reads sequenced from dissected target C in pup X1 at age P14


title: P14_X2_A: Sindbis reads sequenced from dissected target A in pup X2 at age P14


title: P14_3_A: Sindbis reads sequenced from dissected target A in pup 3 at age P14


title: P14_3_C: Sindbis reads sequenced from dissected target C in pup 3 at age P14


title: P14_X1_A: Sindbis reads sequenced from dissected target A in pup X1 at age P14


title: P14_B1_M: Sindbis reads sequenced from dissected target M in pup B1 at age P14


title: P14_B1_Sub: Sindbis reads sequenced from dissected target Sub in pup B1 at age P14


title: P14_B1_C: Sindbis reads sequenced from dissected target C in pup B1 at age P14


title: Sindbis reads sequenced from dissected Subcortical targets in pup U at age P7

data_processing:
Library strategy: MAP-seq
reads were parsed to extract: sindbis barcode (nucleotide 1-32), sinbis index (nuceodite 89-94), and umi sequence (nucleotide 95-106).
reads are deduplicated on the base of the UMI sequence
reads are tagged as viral, spike or unknown depending on their barcode sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
barcodes from the injection site are clustered to correct for sequencing errors
barcodes from the target regions are mapped to the error-corrected barcodes found in the injection sites
counts are normalized with the number of spike found in the same target region
Genome_build: no genome mapping (this is a barcode matching protocol)
Supplementary_files_format_and_content: mapseq.tsv.gz contains the result of the parsing of the sindbis reads. The file report the amount of unique umi sequence of a target that was associated to a barcode of the injection site. It also report include the number of spike in the region and te number of time the barcode was seen in th injection site.

source_name: cortex

value: U

value: cortex


title: P14_B1_A: Sindbis reads sequenced from dissected target A in pup B1 at age P14


title: Sindbis reads sequenced from dissected target S2 in pup U at age P7


title: Sindbis reads sequenced from dissected target A in pup U at age P7


title: Sindbis reads sequenced from dissected Contralateral targets in pup U at age P7


title: P14_A1_Sub: Sindbis reads sequenced from dissected target Sub in pup A1 at age P14


title: Sindbis reads sequenced from dissected target M in pup U at age P7


title: P14_A1_V: Sindbis reads sequenced from dissected target V in pup A1 at age P14


title: Sindbis reads sequenced from dissected Subcortical targets in pup T at age P7

value: T


title: Sindbis reads sequenced from dissected target V in pup T at age P7


title: Sindbis reads sequenced from dissected target M in pup T at age P7


title: P14_X1_Sub: Sindbis reads sequenced from dissected target Sub in pup X1 at age P14


title: Sindbis reads sequenced from dissected target S2 in pup T at age P7


title: P14_3_M: Sindbis reads sequenced from dissected target M in pup 3 at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup N at age P7

value: N


title: Sindbis reads sequenced from dissected target V in pup U at age P7


title: Sindbis reads sequenced from dissected Subcortical targets in pup N at age P7


title: P14_A1_A: Sindbis reads sequenced from dissected target A in pup A1 at age P14


title: Sindbis reads sequenced from dissected target V in pup N at age P7


title: P14_A1_M: Sindbis reads sequenced from dissected target M in pup A1 at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup U at age P7


title: Sindbis reads sequenced from dissected Contralateral targets in pup N at age P7


title: Sindbis reads sequenced from dissected target V in pup M at age P7


title: Sindbis reads sequenced from dissected Contralateral targets in pup T at age P7


title: Sindbis reads sequenced from dissected target A in pup T at age P7


title: Sindbis reads sequenced from dissected Subcortical targets in pup M at age P7


title: Sindbis reads sequenced from dissected target S2 in pup N at age P7


title: Sindbis reads sequenced from dissected target M in pup N at age P7


title: Sindbis reads sequenced from dissected target S2 in pup M at age P7


title: Sindbis reads sequenced from dissected Contralateral targets in pup M at age P7


title: Sindbis reads sequenced from dissected target M in pup M at age P7


title: Sindbis reads sequenced from dissected injection site S1 in pup T at age P7


title: Sindbis reads sequenced from dissected target A in pup M at age P7


title: Sindbis reads sequenced from dissected injection site S1 in pup D at age P5

value: D


title: Sindbis reads sequenced from dissected target V in pup D at age P5


title: Sindbis reads sequenced from dissected target A in pup N at age P7


title: Sindbis reads sequenced from dissected target S2 in pup D at age P5


title: Sindbis reads sequenced from dissected Contralateral targets in pup D at age P5


title: Sindbis reads sequenced from dissected Subcortical targets in pup D at age P5


title: Sindbis reads sequenced from dissected target A in pup D at age P5


title: Sindbis reads sequenced from dissected Subcortical targets in pup 4 at age P5


title: Sindbis reads sequenced from dissected injection site S1 in pup 4 at age P5


title: Sindbis reads sequenced from dissected target V in pup 4 at age P5


title: Sindbis reads sequenced from dissected Contralateral targets in pup 4 at age P5


title: Sindbis reads sequenced from dissected target S2 in pup 4 at age P5


title: Sindbis reads sequenced from dissected target A in pup 4 at age P5


title: Sindbis reads sequenced from dissected target M in pup D at age P5


title: Sindbis reads sequenced from dissected target M in pup 4 at age P5


title: Sindbis reads sequenced from dissected injection site S1 in pup M at age P7


title: Sindbis reads sequenced from dissected Subcortical targets in pup 3 at age P5


title: Sindbis reads sequenced from dissected target S2 in pup 3 at age P5


title: Sindbis reads sequenced from dissected Contralateral targets in pup 3 at age P5


title: Sindbis reads sequenced from dissected injection site S1 in pup 3 at age P5


title: Sindbis reads sequenced from dissected target M in pup 3 at age P5


title: Sindbis reads sequenced from dissected target A in pup 3 at age P5


title: Sindbis reads sequenced from dissected Subcortical targets in pup 2 at age P5


title: Sindbis reads sequenced from dissected target S2 in pup 2 at age P5


title: Sindbis reads sequenced from dissected Contralateral targets in pup 2 at age P5


title: Sindbis reads sequenced from dissected Subcortical targets in pup W at age P14

value: W


title: Sindbis reads sequenced from dissected injection site S1 in pup 2 at age P5


title: Sindbis reads sequenced from dissected target S2 in pup W at age P14


title: Sindbis reads sequenced from dissected target V in pup W at age P14


title: Sindbis reads sequenced from dissected target M in pup W at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup W at age P14


title: Sindbis reads sequenced from dissected target A in pup 2 at age P5


title: Sindbis reads sequenced from dissected target M in pup 2 at age P5


title: Sindbis reads sequenced from dissected target V in pup 3 at age P5


title: Sindbis reads sequenced from dissected target V in pup V at age P14


title: Sindbis reads sequenced from dissected Contralateral targets in pup W at age P14


title: Sindbis reads sequenced from dissected target A in pup W at age P14


title: Sindbis reads sequenced from dissected Subcortical targets in pup V at age P14


title: Sindbis reads sequenced from dissected target M in pup V at age P14


title: Sindbis reads sequenced from dissected target S2 in pup V at age P14


title: Sindbis reads sequenced from dissected Contralateral targets in pup V at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup V at age P14


title: Sindbis reads sequenced from dissected target A in pup V at age P14


title: Sindbis reads sequenced from dissected target V in pup 2 at age P5


title: Sindbis reads sequenced from dissected target V in pup R at age P14

value: R


title: Sindbis reads sequenced from dissected target A in pup R at age P14


title: Sindbis reads sequenced from dissected Subcortical targets in pup R at age P14


title: Sindbis reads sequenced from dissected target M in pup R at age P14


title: Sindbis reads sequenced from dissected target S2 in pup R at age P14


title: Sindbis reads sequenced from dissected target V in pup Q at age P14

value: Q


title: Sindbis reads sequenced from dissected Contralateral targets in pup R at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup R at age P14


title: Sindbis reads sequenced from dissected Subcortical targets in pup Q at age P14


title: Sindbis reads sequenced from dissected target M in pup Q at age P14


title: Sindbis reads sequenced from dissected target S2 in pup Q at age P14


title: Sindbis reads sequenced from dissected injection site S1 in pup Q at age P14


title: Sindbis reads sequenced from dissected Contralateral targets in pup Q at age P14


title: Sindbis reads sequenced from dissected target A in pup Q at age P14


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 280, P21 [Sc_280]

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

description:
processed data file:
samples_normScaledReadsPerBase.csv

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2 (-Q 5)
RNA-seq read quantification was performed using Kallisto 0.43.0 (-b 50 –single -l 200 -s 20)
DEG calling was performed using Sleuth 0.28.1 (Control contrast)
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file with gene abundance for all samples
samples_normScaledReadsPerBase.csv: csv (Normalized scaled reads per base for each sample)

source_name: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse_spinal cord

extract_protocol:
Spinal cords were removed, flash frozen under liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA-Seq libraries were constructed using either Illumina TruSeq Sample Prep Kit or the NEXTflex Rapid Directional RNA-Seq Kit as per manufacturer's directions. The subset of samples for which each protocol was used is mentioned against each sample in the SAMPLES section

tag: gender

value: Male

tag: genotype/variatation

value: Cnp-Cre; Tardbp-fl/fl

tag: age

value: Spinal Cord

tag: library preparation

value: Illumina TruSeq RNA Sample Prep Kit


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 270, P21 [Sc_270]

value: Female


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 1174, P21 [Sc_1174]


title: Control- TDP-43 floxed mouse ID 715, P21 [Sc_715]

source_name: Control TDP-43 floxed mouse_spinal cord

value: Tardbp-fl/fl


title: Oligodendrocyte specific, TDP-43 homozygous conditional knockout mouse ID 277, P21 [Sc_277]


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 275, P21 [Sc_275]

source_name: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse_spinal cord

value: Cnp-Cre; Tardbp-fl/+


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 716, P21 [Sc_716]


title: Retina_Diabetic_rep3_Input

city: shanghai

first: xinping

last: she

state: shanghai

address: shanghai

department: Ophthalmology

country: China

institute: Department of Ophthalmology,Shanghai General Hospital,Shanghai Jiao Tong University School of Medicine

data_processing:
Library strategy: MeRIP-Seq
Base calling were performed with Illumina CASAVA pipeline
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11). In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
Peak finding algorithm to indentify regions of IP enrichment over background used the MACS2 version 2.1.0 . A q value threshold of enrichment of 0.05 was used for all data sets. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis.
Genome_build: ftp://ftp.ensembl.org/pub/release- 74/fasta/rattus_norvegicus/dna/
Supplementary_files_format_and_content: tab-delimited text files include fold-enrichment values for each sample

organism: Rattus norvegicus

source_name: Retina

growth_protocol: Feeding conditions are that the ammonia concentration is less than 20ppm, the relative humidity is 40-60%, and the room temperature is maintained at 22-24℃.

extract_protocol:
RNA was harvested using Trizol reagent, and 2 μg of total RNA for the construction of sequencing libraries.
Fragmented RNA (~100 nt) was incubated with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina platform.

treatment_protocol: For Sprague-Dawley rat (100g, male), either streptozotocin (STZ, Sigma, St. Louis, MO, 60 mg/kg STZ after fasting for 12 h) or vehicle (citrate buffer control) was injected intraperitoneally for five consecutive days. The fasting blood glucose was tested 1 week after the last STZ injection, and the value >16.7 mmol/L were considered diabetic.

value: Sprague-Dawley

value: retina

tag: genotype

value: Diabetic

tag: weight

tag: agent

value: streptozotocin (STZ, Sigma, St. Louis, MO, 60 mg/kg STZ after fasting for 12 h) was injected intraperitoneally for five consecutive days


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 276, P21 [Sc_276]


title: Retina_WT_rep2_Input

value: WT

value: vehicle (citrate buffer control) was injected intraperitoneally for five consecutive days


title: Control- TDP-43 floxed mouse ID 1142, P21 [Sc_1142]


title: Control- TDP-43 floxed mouse ID 723, P21 [Sc_723]


title: Control- TDP-43 floxed mouse ID 854, P21 [Sc_854]


title: Retina_WT_rep2_IP


title: Retina  Diabetic rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rat whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ftp://ftp.ensembl.org/pub/release- 74/fasta/rattus_norvegicus/dna/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.
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® Ultra 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). 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 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 ml USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in 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. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.


title: Retina  Diabetic rep2


title: Retina_Diabetic_rep2_Input


title: Retina  Diabetic rep1


title: Retina WT rep3


title: Retina_WT_rep3_Input


title: Retina_Diabetic_rep1_Input


title: Retina_Diabetic_rep3_IP


title: Retina WT rep2


title: Retina_Diabetic_rep2_IP


title: Retina_WT_rep1_Input


title: Retina_WT_rep1_IP


title: Retina WT rep1


title: Oligodendrocyte specific, TDP-43 heterozygous conditional knockout mouse ID 272, P21 [Sc_272]


title: Yellow [miRNA-seq]

city: Yaan

first: jideng

last: Ma

address: Xinkang road

institute: Sichuan Agricultural University(SICAU),

description: microRNA derived from yellow skin  tissue of Botia superciliaris

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to Zebrafish reference genome with stringent criteria.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: Danio rerio (assembly GRCz11).miRbase release 21
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Sinibotia superciliaris

source_name: Skin

growth_protocol: Wild B. superciliaris were captured from the Chin-sha River watershed , Fish (average initial weight: 6.25 ± 0.30 g, length: 8.75 ± 0.20 cm)

extract_protocol:
RNA was harvested using Trizol reagent.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Black and yellow skin tissue samples were collected from 6 individuals . All fresh skin tissue samples were immediately frozen in liquid nitrogen and then stored at −80 °C before RNA isolation.

value: Yellow skin

tag: developmental stage

value: adult


title: Retina_WT_rep3_IP


title: C. chinense Flower

city: New Delhi

first: Nirala

last: Ramchiary

address: lab-229, school of life sciences, JNU, New Delhi - 110067

department: School of life sciences

country: India

institute: Jawaharlal Nehru University

data_processing:
miRNA profiling
Supplementary_files_format_and_content: miRNAs and counts

organism: Capsicum chinense

source_name: Flower

growth_protocol: For small RNA, one genotype each from Bhut jolokia (C. chinense) and C. frutescens (Accesion 4) with contrasting fruit characters was selected. The seeds of Bhut jolokia and Acc. 4 were surface sterilized with 4% sodium hypochlorite, germinated in the petri-dish using moist germination paper and transfer to glass house in pots after one week and grown at 24-26°C with 16 hours light period until fruit setting and maturity. For fruit tissues, samples were collected at various fruit developmental stages such as 5 Day Post Anthesis (DPA), 10DPA, 20DPA, Breaker (30-45DPA), and Mature (45-60 DPA). All the fruit stages were pooled and considered as the fruit tissue sample. The fully expanded fresh leaf and flower buds of different size and age along with stem were collected from healthy matured glass house grown plants.

extract_protocol:
The RNA Extraction was carried out using Macherey-Nagel NucleoSpin RNA kit (MN, US). The total RNA were pooled from the three biological replicates from the individual tissue samples. Further, the quality, and the quantity of RNAs was estimated with Bioanalyzer (Agilent) plant Nano kit.
For small RNA library preparation, RNA samples with 260/280 ratio of 1.9–2.0 and RNA integrity number (RIN) of ≥ 8 were selected. The sRNA libraries were prepared by using TruSeq Small RNA sample preparation kit (Illumina, US). Each sRNA library was sequenced using Illumina Genome Analyser II at Genotypic Technologies Pvt. Ltd, Bangalore, India.

value: Flower


title: C. chinense Stem

source_name: Stem

value: Stem


title: C. chinense Leaf

source_name: Leaf

value: Leaf


title: C. chinense Fruit

source_name: Fruit

value: Fruit


title: Retina_Diabetic_rep1_IP


title: adult whole brain B15

city: Palavas

first: Mélanie

last: Blanc

address: Route de Maguelone

department: UMR MARBEC

country: France

institute: INRAE

description:
corrected_matrix.csv ID: B15
library pool: P6-1

data_processing:
Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1
Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with "L,0,-0.6". Rk due to batch effects described below, PE sequences were analyzed as SE.
methyl calling using Bismark extractor, cov >= 5 (processed data files)
batch correction using ComBat (see supplementary data corrected_matrix.csv)
identification of DMRs using Methylkit R v1.12; (300 bp tiles with at least 4 C included and >=10% differential methylation)
Genome_build: DanRer11
Supplementary_files_format_and_content: methyl call (cov >= 5) from bismark methyl extractor.  *.tabular files (before correction) and corrected_matrix.csv (after correction)

organism: Danio rerio

source_name: adult whole brain

extract_protocol: Fish were euthanized, brains were dissected and flash frozen in liquid nitrogen, and DNA was extracted using TriPrep extraction kit (Macherey-Nagel). 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE, University of Perpignan, France, for pair-ended or single ended RRBS

value: AB line

tag: generation

tag: Sex

value: M


title: adult whole brain B11

description:
corrected_matrix.csv ID: B11
library pool: P5-3

value: F


title: Yellow [RNA-seq]

description: mRNA derived from yellow skin  tissue of Botia superciliaris

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to Zebrafish reference genome with stringent criteria.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: Danio rerio (assembly GRCz11).
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

extract_protocol:
RNA was harvested using Trizol reagent.
mRNA libraries were prepared for sequencing using standard Illumina protocols


title: Black [RNA-seq]

description: mRNA derived from black skin  tissue of Botia superciliaris

value: Black skin


title: adult whole brain B10

description:
corrected_matrix.csv ID: B10
library pool: P5-2


title: adult whole brain B16

description:
corrected_matrix.csv ID: B16
library pool: P6-2


title: Black [miRNA-seq]

description: microRNA derived from black skin  tissue of Botia superciliaris


title: adult whole brain B12

description:
corrected_matrix.csv ID: B12
library pool: P5-4


title: adult whole brain B5

description:
corrected_matrix.csv ID: B5
library pool: P4-3


title: adult whole brain B7

description:
corrected_matrix.csv ID: B7
library pool: P4-5


title: adult whole brain B6

description:
corrected_matrix.csv ID: B6
library pool: P4-4


title: adult whole brain B13

description:
corrected_matrix.csv ID: B13
library pool: P5-5


title: adult whole brain B3

description:
corrected_matrix.csv ID: B3
library pool: P4-1


title: adult whole brain B4

description:
corrected_matrix.csv ID: B4
library pool: P4-2


title: adult whole brain B2

description:
corrected_matrix.csv ID: B2
library pool: P3-6


title: adult whole brain B9

description:
corrected_matrix.csv ID: B9
library pool: P5-1


title: adult whole brain B1

description:
corrected_matrix.csv ID: B1
library pool: P3-5


title: adult whole brain C16

description:
corrected_matrix.csv ID: C16
library pool: P8-6


title: adult whole brain C12

description:
corrected_matrix.csv ID: C12
library pool: P8-2


title: adult whole brain C14

description:
corrected_matrix.csv ID: C14
library pool: P8-4


title: adult whole brain C15

description:
corrected_matrix.csv ID: C15
library pool: P8-5


title: adult whole brain C13

description:
corrected_matrix.csv ID: C13
library pool: P8-3


title: adult whole brain C11

description:
corrected_matrix.csv ID: C11
library pool: P8-1


title: adult whole brain B14

description:
corrected_matrix.csv ID: B14
library pool: P5-6


title: adult whole brain C10

description:
corrected_matrix.csv ID: C10
library pool: P7-6


title: adult whole brain C8

description:
corrected_matrix.csv ID: C8
library pool: P7-4


title: adult whole brain C9

description:
corrected_matrix.csv ID: C9
library pool: P7-5


title: adult whole brain C7

description:
corrected_matrix.csv ID: C7
library pool: P7-3


title: adult whole brain C3

description:
corrected_matrix.csv ID: C3
library pool: P6-5


title: adult whole brain A13

description:
corrected_matrix.csv ID: A13
library pool: P3-1


title: adult whole brain C5

description:
corrected_matrix.csv ID: C5
library pool: P7-1


title: adult whole brain B8

description:
corrected_matrix.csv ID: B8
library pool: P4-6


title: adult whole brain A15

description:
corrected_matrix.csv ID: A15
library pool: P3-3


title: adult whole brain A12

description:
corrected_matrix.csv ID: A12
library pool: P2-6


title: adult whole brain C1

description:
corrected_matrix.csv ID: C1
library pool: P6-3


title: adult whole brain A16

description:
corrected_matrix.csv ID: A16
library pool: P3-4


title: adult whole brain C2

description:
corrected_matrix.csv ID: C2
library pool: P6-4


title: adult whole brain A3

description:
corrected_matrix.csv ID: A3
library pool: P1-3


title: adult whole brain A2

description:
corrected_matrix.csv ID: A2
library pool: P1-2


title: adult whole brain A10

description:
corrected_matrix.csv ID: A10
library pool: P2-4


title: adult whole brain A7

description:
corrected_matrix.csv ID: A7
library pool: P2-1


title: adult whole brain A11

description:
corrected_matrix.csv ID: A11
library pool: P2-5


title: adult whole brain A14

description:
corrected_matrix.csv ID: A14
library pool: P3-2


title: adult whole brain A6

description:
corrected_matrix.csv ID: A6
library pool: P1-6


title: adult whole brain A4

description:
corrected_matrix.csv ID: A4
library pool: P1-4


title: adult whole brain A5

description:
corrected_matrix.csv ID: A5
library pool: P1-5


title: adult whole brain A1

description:
corrected_matrix.csv ID: A1
library pool: P1-1


title: adult whole brain C6

description:
corrected_matrix.csv ID: C6
library pool: P7-2


title: adult whole brain C4

description:
corrected_matrix.csv ID: C4
library pool: P6-6


title: adult whole brain A9

description:
corrected_matrix.csv ID: A9
library pool: P2-3