title: mouse muscle ischemia d21 SS2_19_278_C3

description:
Smartseq2
SS2_19_278_C3


title: mouse muscle ischemia d21 SS2_19_278_C6

status: Public on Apr 08 2024

type: SRA

city: Uppsala

first: Feifei

last: Xu

address: Husargatan 3

country: Sweden

institute: Uppsala University

description:
Smartseq2
SS2_19_278_C6

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was converted to demultiplexed FASTQ files using deindexer (https://github.com/ws6/deindexer) based on the Nextera index adapters and the 384 well layout.
Reads were then aligned to the mouse genome (GRCm38) using STAR v2.7.7a (Dobin et al., 2013), and FeatureCounts v2.0.1 (Liao et al., 2014) was subsequently used to extract raw gene expression counts matrix from the algnments.
Scanpy v1.7.1 package (Wolf et al., 2018) was used to convert the resulting cells-by-genes table to AnnData object and for further analysis for scRNA-seq data. Cell libraries were filtered out if: (1) the percentages of mitochondrial and ribosomal gene families were above 10%; (2) the number of unique genes in a cell was below 500; (3) predicted doublet by Scrublet v0.2.3 (Wolock et al., 2019). In total, 1425 cells were retained for downstream analysis. Genes detected in less than three cells along with mitochondrial genes were excluded from the analysis, leaving 38,178 genes in count matrix.
Python version of velocyto v0.17.17 (La Manno et al., 2018) run_smartseq2 command was used to count unspliced transcripts from the alignments masking out expressed repeat annotation downloaded from UCSC genome browser. The resulting loom file was read and the unspliced counts were added to AnnData object in ‘layers’ using scvelo v0.2.4 (Bergen et al., 2020)
Assembly: GRCh38, vM25
Supplementary files format and content: matrix.csv stores the gene by cell count matrix, with its correpsonding metadata meta.csv; adata file is an anndata object that contains the count matrix, meta data, spliced and unspliced counts and umap coordinates.

molecule: total RNA

organism: Mus musculus

source_name: gastrocnemous muscle

growth_protocol: Cx3cr1-CreERT2 mice (Yona et al., 2013) were crossed with R26-TdTomato mice (Madisen et al., 2010), resulting in a heritable expression of tdTomato in myeloid cells and tissue-resident macrophages upon tamoxifen administration. For simultaneous in situ detection of PDGFRβ expression, the generated mouse line was crossed with the PdgfrβeGFP reporter mouse line.

extract_protocol:
Ischemic gastrocnemius muscle was removed and minced into very small pieces with a scalpel. The tissue was then mechanically and enzymatically dissociated by incubating in collagenase II (500 U/ml) (#17101015; Gibco) in RPMI1640 in 37°C for 30 minutes during intermittent pipetting. After washing the tissue with ice-cold DPBS, it was incubated for further 30 minutes with collagenase IV (15 U/ml) (#17104019; Gibco) and dispase (2.4 U/ml) (#17105041; Gibco) in RPMI1640, with intermittent pipetting. Thereafter, the tissue suspension was passed through a 23G 0.6 mm needle 8-10 times, and filtered through a 70 µm cell strainer. Once a single-cell suspension was obtained, live/dead cell staining was carried out using CellTrace Calcein Violet, AM (C34858; Invitrogen), according to manufacturer’s instructions. Lastly, tdTomato+PDGFRβ+/- cells and tdTomato-PDGFRβ+ cells were FACS sorted into SMART-Seq2 plates, using BD FACSAria™ III Cell Sorter with 4 lasers configuration (405, 488, 561, 633 nm) (BD Biosciences).
RNA libraries were prepared according to Smart-seq2 protocol.

treatment_protocol: CreERT2-mediated recombination was initiated by oral gavage of 2 mg of tamoxifen (Sigma) in corn oil once every 24 hours for 5 days, followed by a 5-days washout period. After this perior, the mice were anesthetized (Isoflurane, 2.5%, Forene, Abbott Laboratories) and the fur was removed from the left leg. Hindlimb ischemia was induced as described before (Niiyama et al., 2009). Briefly, the left femoral artery was separated from the femoral vein, followed by ligation and cutting of the femoral artery above the superficial epigastric artery branch. Post-operative pain relief was achieved with sub-cutaneous administration of carprofen (5 mg/kg). Animals were terminated by cervical dislocation before gastrocnemius muscle extraction.

tag: tissue

value: gastrocnemous muscle

tag: Sex

value: female

tag: genotype

tag: treatment

value: Hindlimb ischemia induction


title: mouse muscle ischemia d21 SS2_19_278_C2

description:
Smartseq2
SS2_19_278_C2


title: mouse muscle ischemia d21 SS2_19_278_B24

description:
Smartseq2
SS2_19_278_B24


title: mouse muscle ischemia d21 SS2_19_278_B22

description:
Smartseq2
SS2_19_278_B22


title: mouse muscle ischemia d21 SS2_19_278_B21

description:
Smartseq2
SS2_19_278_B21


title: mouse muscle ischemia d21 SS2_19_278_B20

description:
Smartseq2
SS2_19_278_B20


title: mouse muscle ischemia d21 SS2_19_278_B18

description:
Smartseq2
SS2_19_278_B18


title: mouse muscle ischemia d21 SS2_19_278_B17

description:
Smartseq2
SS2_19_278_B17


title: mouse muscle ischemia d21 SS2_19_278_B16

description:
Smartseq2
SS2_19_278_B16


title: mouse muscle ischemia d21 SS2_19_278_B14

description:
Smartseq2
SS2_19_278_B14


title: mouse muscle ischemia d21 SS2_19_278_B12

description:
Smartseq2
SS2_19_278_B12


title: mouse muscle ischemia d21 SS2_19_278_C15

description:
Smartseq2
SS2_19_278_C15


title: mouse muscle ischemia d21 SS2_19_278_C11

description:
Smartseq2
SS2_19_278_C11


title: mouse muscle ischemia d21 SS2_19_278_B8

description:
Smartseq2
SS2_19_278_B8


title: mouse muscle ischemia d21 SS2_19_278_B9

description:
Smartseq2
SS2_19_278_B9


title: mouse muscle ischemia d21 SS2_19_278_B11

description:
Smartseq2
SS2_19_278_B11


title: mouse muscle ischemia d21 SS2_19_278_B7

description:
Smartseq2
SS2_19_278_B7


title: mouse muscle ischemia d21 SS2_19_278_B10

description:
Smartseq2
SS2_19_278_B10


title: mouse muscle ischemia d21 SS2_19_278_C7

description:
Smartseq2
SS2_19_278_C7


title: mouse muscle ischemia d21 SS2_19_278_B5

description:
Smartseq2
SS2_19_278_B5


title: mouse muscle ischemia d21 SS2_19_278_B3

description:
Smartseq2
SS2_19_278_B3


title: mouse muscle ischemia d21 SS2_19_278_B2

description:
Smartseq2
SS2_19_278_B2


title: mouse muscle ischemia d21 SS2_19_278_B4

description:
Smartseq2
SS2_19_278_B4


title: mouse muscle ischemia d21 SS2_19_278_A23

description:
Smartseq2
SS2_19_278_A23


title: mouse muscle ischemia d21 SS2_19_278_A24

description:
Smartseq2
SS2_19_278_A24


title: mouse muscle ischemia d21 SS2_19_278_B23

description:
Smartseq2
SS2_19_278_B23


title: mouse muscle ischemia d21 SS2_19_278_C1

description:
Smartseq2
SS2_19_278_C1


title: mouse muscle ischemia d21 SS2_19_278_B19

description:
Smartseq2
SS2_19_278_B19


title: mouse muscle ischemia d21 SS2_19_278_A21

description:
Smartseq2
SS2_19_278_A21


title: mouse muscle ischemia d21 SS2_19_278_A22

description:
Smartseq2
SS2_19_278_A22


title: mouse muscle ischemia d21 SS2_19_278_B13

description:
Smartseq2
SS2_19_278_B13


title: mouse muscle ischemia d21 SS2_19_278_A19

description:
Smartseq2
SS2_19_278_A19


title: mouse muscle ischemia d21 SS2_19_278_B15

description:
Smartseq2
SS2_19_278_B15


title: mouse muscle ischemia d21 SS2_19_278_A18

description:
Smartseq2
SS2_19_278_A18


title: mouse muscle ischemia d21 SS2_19_278_A20

description:
Smartseq2
SS2_19_278_A20


title: mouse muscle ischemia d21 SS2_19_278_A17

description:
Smartseq2
SS2_19_278_A17


title: mouse muscle ischemia d21 SS2_19_278_A15

description:
Smartseq2
SS2_19_278_A15


title: mouse muscle ischemia d21 SS2_19_278_A16

description:
Smartseq2
SS2_19_278_A16


title: mouse muscle ischemia d21 SS2_19_278_A14

description:
Smartseq2
SS2_19_278_A14


title: mouse muscle ischemia d21 SS2_19_278_A12

description:
Smartseq2
SS2_19_278_A12


title: mouse muscle ischemia d21 SS2_19_278_A13

description:
Smartseq2
SS2_19_278_A13


title: mouse muscle ischemia d21 SS2_19_278_A9

description:
Smartseq2
SS2_19_278_A9


title: mouse muscle ischemia d21 SS2_19_278_A10

description:
Smartseq2
SS2_19_278_A10


title: mouse muscle ischemia d21 SS2_19_278_A11

description:
Smartseq2
SS2_19_278_A11


title: mouse muscle ischemia d21 SS2_19_278_B6

description:
Smartseq2
SS2_19_278_B6


title: mouse muscle ischemia d21 SS2_19_278_A8

description:
Smartseq2
SS2_19_278_A8


title: mouse muscle ischemia d21 SS2_19_278_A7

description:
Smartseq2
SS2_19_278_A7


title: mouse muscle ischemia d21 SS2_19_278_B1

description:
Smartseq2
SS2_19_278_B1


title: mouse muscle ischemia d21 SS2_19_278_A6

description:
Smartseq2
SS2_19_278_A6


title: mouse muscle ischemia d21 SS2_19_278_A5

description:
Smartseq2
SS2_19_278_A5


title: mouse muscle ischemia d21 SS2_19_278_A4

description:
Smartseq2
SS2_19_278_A4


title: mouse muscle ischemia d21 SS2_19_278_A3

description:
Smartseq2
SS2_19_278_A3


title: mouse muscle ischemia d21 SS2_19_278_A2

description:
Smartseq2
SS2_19_278_A2


title: mouse muscle ischemia d21 SS2_19_278_A1

description:
Smartseq2
SS2_19_278_A1


title: mouse muscle ischemia d21 SS2_19_276_P22

description:
Smartseq2
SS2_19_276_P22

value: male


title: mouse muscle ischemia d21 SS2_19_276_P20

description:
Smartseq2
SS2_19_276_P20


title: mouse muscle ischemia d21 SS2_19_276_P18

description:
Smartseq2
SS2_19_276_P18


title: mouse muscle ischemia d21 SS2_19_276_P17

description:
Smartseq2
SS2_19_276_P17


title: mouse muscle ischemia d21 SS2_19_276_P16

description:
Smartseq2
SS2_19_276_P16


title: mouse muscle ischemia d21 SS2_19_276_P15

description:
Smartseq2
SS2_19_276_P15


title: mouse muscle ischemia d21 SS2_19_276_P14

description:
Smartseq2
SS2_19_276_P14


title: mouse muscle ischemia d21 SS2_19_276_P21

description:
Smartseq2
SS2_19_276_P21


title: mouse muscle ischemia d21 SS2_19_276_P13

description:
Smartseq2
SS2_19_276_P13


title: mouse muscle ischemia d21 SS2_19_276_P11

description:
Smartseq2
SS2_19_276_P11


title: mouse muscle ischemia d21 SS2_19_276_P12

description:
Smartseq2
SS2_19_276_P12


title: mouse muscle ischemia d21 SS2_19_276_P19

description:
Smartseq2
SS2_19_276_P19


title: mouse muscle ischemia d21 SS2_19_276_P10

description:
Smartseq2
SS2_19_276_P10


title: mouse muscle ischemia d21 SS2_19_276_P9

description:
Smartseq2
SS2_19_276_P9


title: mouse muscle ischemia d21 SS2_19_276_P8

description:
Smartseq2
SS2_19_276_P8


title: mouse muscle ischemia d21 SS2_19_276_P7

description:
Smartseq2
SS2_19_276_P7


title: mouse muscle ischemia d21 SS2_19_276_P6

description:
Smartseq2
SS2_19_276_P6


title: mouse muscle ischemia d21 SS2_19_276_P5

description:
Smartseq2
SS2_19_276_P5


title: mouse muscle ischemia d21 SS2_19_276_P1

description:
Smartseq2
SS2_19_276_P1


title: mouse muscle ischemia d21 SS2_19_276_P2

description:
Smartseq2
SS2_19_276_P2


title: mouse muscle ischemia d21 SS2_19_276_P3

description:
Smartseq2
SS2_19_276_P3


title: mouse muscle ischemia d21 SS2_19_276_O22

description:
Smartseq2
SS2_19_276_O22


title: mouse muscle ischemia d21 SS2_19_276_O23

description:
Smartseq2
SS2_19_276_O23


title: mouse muscle ischemia d21 SS2_19_276_O19

description:
Smartseq2
SS2_19_276_O19


title: mouse muscle ischemia d21 SS2_19_276_O18

description:
Smartseq2
SS2_19_276_O18


title: mouse muscle ischemia d21 SS2_19_276_O20

description:
Smartseq2
SS2_19_276_O20


title: mouse muscle ischemia d21 SS2_19_276_O15

description:
Smartseq2
SS2_19_276_O15


title: mouse muscle ischemia d21 SS2_19_276_O16

description:
Smartseq2
SS2_19_276_O16


title: mouse muscle ischemia d21 SS2_19_276_O14

description:
Smartseq2
SS2_19_276_O14


title: mouse muscle ischemia d21 SS2_19_276_O24

description:
Smartseq2
SS2_19_276_O24


title: mouse muscle ischemia d21 SS2_19_276_O12

description:
Smartseq2
SS2_19_276_O12


title: mouse muscle ischemia d21 SS2_19_276_O13

description:
Smartseq2
SS2_19_276_O13


title: mouse muscle ischemia d21 SS2_19_276_O10

description:
Smartseq2
SS2_19_276_O10


title: mouse muscle ischemia d21 SS2_19_276_O9

description:
Smartseq2
SS2_19_276_O9


title: mouse muscle ischemia d21 SS2_19_276_O8

description:
Smartseq2
SS2_19_276_O8


title: mouse muscle ischemia d21 SS2_19_276_O5

description:
Smartseq2
SS2_19_276_O5


title: mouse muscle ischemia d21 SS2_19_276_O7

description:
Smartseq2
SS2_19_276_O7


title: mouse muscle ischemia d21 SS2_19_276_O4

description:
Smartseq2
SS2_19_276_O4


title: mouse muscle ischemia d21 SS2_19_276_O6

description:
Smartseq2
SS2_19_276_O6


title: mouse muscle ischemia d21 SS2_19_276_P4

description:
Smartseq2
SS2_19_276_P4


title: mouse muscle ischemia d21 SS2_19_276_O3

description:
Smartseq2
SS2_19_276_O3


title: mouse muscle ischemia d21 SS2_19_276_O1

description:
Smartseq2
SS2_19_276_O1


title: mouse muscle ischemia d21 SS2_19_276_O2

description:
Smartseq2
SS2_19_276_O2


title: mouse muscle ischemia d21 SS2_19_276_O21

description:
Smartseq2
SS2_19_276_O21


title: mouse muscle ischemia d21 SS2_19_276_O17

description:
Smartseq2
SS2_19_276_O17


title: mouse muscle ischemia d21 SS2_19_276_N23

description:
Smartseq2
SS2_19_276_N23


title: mouse muscle ischemia d21 SS2_19_276_N21

description:
Smartseq2
SS2_19_276_N21


title: mouse muscle ischemia d21 SS2_19_276_N22

description:
Smartseq2
SS2_19_276_N22


title: mouse muscle ischemia d21 SS2_19_276_N20

description:
Smartseq2
SS2_19_276_N20


title: mouse muscle ischemia d21 SS2_19_276_N24

description:
Smartseq2
SS2_19_276_N24


title: mouse muscle ischemia d21 SS2_19_276_N19

description:
Smartseq2
SS2_19_276_N19


title: mouse muscle ischemia d21 SS2_19_276_N18

description:
Smartseq2
SS2_19_276_N18


title: mouse muscle ischemia d21 SS2_19_276_N17

description:
Smartseq2
SS2_19_276_N17


title: mouse muscle ischemia d21 SS2_19_276_N16

description:
Smartseq2
SS2_19_276_N16


title: mouse muscle ischemia d21 SS2_19_276_N15

description:
Smartseq2
SS2_19_276_N15


title: mouse muscle ischemia d21 SS2_19_276_N14

description:
Smartseq2
SS2_19_276_N14


title: mouse muscle ischemia d21 SS2_19_276_N13

description:
Smartseq2
SS2_19_276_N13


title: mouse muscle ischemia d21 SS2_19_276_N12

description:
Smartseq2
SS2_19_276_N12


title: mouse muscle ischemia d21 SS2_19_276_N9

description:
Smartseq2
SS2_19_276_N9


title: mouse muscle ischemia d21 SS2_19_276_N10

description:
Smartseq2
SS2_19_276_N10


title: mouse muscle ischemia d21 SS2_19_276_N8

description:
Smartseq2
SS2_19_276_N8


title: mouse muscle ischemia d21 SS2_19_276_N11

description:
Smartseq2
SS2_19_276_N11


title: mouse muscle ischemia d21 SS2_19_276_N7

description:
Smartseq2
SS2_19_276_N7


title: mouse muscle ischemia d21 SS2_19_276_N6

description:
Smartseq2
SS2_19_276_N6


title: mouse muscle ischemia d21 SS2_19_276_N5

description:
Smartseq2
SS2_19_276_N5


title: mouse muscle ischemia d21 SS2_19_276_N4

description:
Smartseq2
SS2_19_276_N4


title: mouse muscle ischemia d21 SS2_19_276_N1

description:
Smartseq2
SS2_19_276_N1


title: mouse muscle ischemia d21 SS2_19_276_M24

description:
Smartseq2
SS2_19_276_M24


title: mouse muscle ischemia d21 SS2_19_276_M23

description:
Smartseq2
SS2_19_276_M23


title: mouse muscle ischemia d21 SS2_19_276_N3

description:
Smartseq2
SS2_19_276_N3


title: mouse muscle ischemia d21 SS2_19_276_M22

description:
Smartseq2
SS2_19_276_M22


title: mouse muscle ischemia d21 SS2_19_276_M20

description:
Smartseq2
SS2_19_276_M20


title: mouse muscle ischemia d21 SS2_19_276_M18

description:
Smartseq2
SS2_19_276_M18


title: mouse muscle ischemia d21 SS2_19_276_M19

description:
Smartseq2
SS2_19_276_M19


title: mouse muscle ischemia d21 SS2_19_276_M16

description:
Smartseq2
SS2_19_276_M16


title: mouse muscle ischemia d21 SS2_19_276_M15

description:
Smartseq2
SS2_19_276_M15


title: mouse muscle ischemia d21 SS2_19_276_M17

description:
Smartseq2
SS2_19_276_M17


title: mouse muscle ischemia d21 SS2_19_276_M13

description:
Smartseq2
SS2_19_276_M13


title: mouse muscle ischemia d21 SS2_19_276_M12

description:
Smartseq2
SS2_19_276_M12


title: mouse muscle ischemia d21 SS2_19_276_M14

description:
Smartseq2
SS2_19_276_M14


title: mouse muscle ischemia d21 SS2_19_276_M6

description:
Smartseq2
SS2_19_276_M6


title: mouse muscle ischemia d21 SS2_19_276_M9

description:
Smartseq2
SS2_19_276_M9


title: mouse muscle ischemia d21 SS2_19_276_M7

description:
Smartseq2
SS2_19_276_M7


title: mouse muscle ischemia d21 SS2_19_276_M8

description:
Smartseq2
SS2_19_276_M8


title: mouse muscle ischemia d21 SS2_19_276_N2

description:
Smartseq2
SS2_19_276_N2


title: mouse muscle ischemia d21 SS2_19_276_M3

description:
Smartseq2
SS2_19_276_M3


title: mouse muscle ischemia d21 SS2_19_276_M2

description:
Smartseq2
SS2_19_276_M2


title: mouse muscle ischemia d21 SS2_19_276_M4

description:
Smartseq2
SS2_19_276_M4


title: mouse muscle ischemia d21 SS2_19_276_M5

description:
Smartseq2
SS2_19_276_M5


title: mouse muscle ischemia d21 SS2_19_276_M21

description:
Smartseq2
SS2_19_276_M21


title: mouse muscle ischemia d21 SS2_19_276_L24

description:
Smartseq2
SS2_19_276_L24


title: mouse muscle ischemia d21 SS2_19_276_L22

description:
Smartseq2
SS2_19_276_L22


title: mouse muscle ischemia d21 SS2_19_276_L23

description:
Smartseq2
SS2_19_276_L23


title: mouse muscle ischemia d21 SS2_19_276_L21

description:
Smartseq2
SS2_19_276_L21


title: mouse muscle ischemia d21 SS2_19_276_L18

description:
Smartseq2
SS2_19_276_L18


title: mouse muscle ischemia d21 SS2_19_276_L16

description:
Smartseq2
SS2_19_276_L16


title: mouse muscle ischemia d21 SS2_19_276_L15

description:
Smartseq2
SS2_19_276_L15


title: mouse muscle ischemia d21 SS2_19_276_L11

description:
Smartseq2
SS2_19_276_L11


title: mouse muscle ischemia d21 SS2_19_276_L20

description:
Smartseq2
SS2_19_276_L20


title: mouse muscle ischemia d21 SS2_19_276_L10

description:
Smartseq2
SS2_19_276_L10


title: mouse muscle ischemia d21 SS2_19_276_L13

description:
Smartseq2
SS2_19_276_L13


title: mouse muscle ischemia d21 SS2_19_276_L19

description:
Smartseq2
SS2_19_276_L19


title: mouse muscle ischemia d21 SS2_19_276_L14

description:
Smartseq2
SS2_19_276_L14


title: mouse muscle ischemia d21 SS2_19_276_L12

description:
Smartseq2
SS2_19_276_L12


title: mouse muscle ischemia d21 SS2_19_276_M10

description:
Smartseq2
SS2_19_276_M10


title: mouse muscle ischemia d21 SS2_19_276_L9

description:
Smartseq2
SS2_19_276_L9


title: mouse muscle ischemia d21 SS2_19_276_M11

description:
Smartseq2
SS2_19_276_M11


title: mouse muscle ischemia d21 SS2_19_276_L8

description:
Smartseq2
SS2_19_276_L8


title: mouse muscle ischemia d21 SS2_19_276_M1

description:
Smartseq2
SS2_19_276_M1


title: mouse muscle ischemia d21 SS2_19_276_K24

description:
Smartseq2
SS2_19_276_K24


title: mouse muscle ischemia d21 SS2_19_276_L2

description:
Smartseq2
SS2_19_276_L2


title: mouse muscle ischemia d21 SS2_19_276_K21

description:
Smartseq2
SS2_19_276_K21


title: mouse muscle ischemia d21 SS2_19_276_L7

description:
Smartseq2
SS2_19_276_L7


title: mouse muscle ischemia d21 SS2_19_276_L17

description:
Smartseq2
SS2_19_276_L17


title: mouse muscle ischemia d21 SS2_19_276_K23

description:
Smartseq2
SS2_19_276_K23


title: mouse muscle ischemia d21 SS2_19_276_L5

description:
Smartseq2
SS2_19_276_L5


title: mouse muscle ischemia d21 SS2_19_276_L6

description:
Smartseq2
SS2_19_276_L6


title: mouse muscle ischemia d21 SS2_19_276_L4

description:
Smartseq2
SS2_19_276_L4


title: mouse muscle ischemia d21 SS2_19_276_K18

description:
Smartseq2
SS2_19_276_K18


title: mouse muscle ischemia d21 SS2_19_276_L3

description:
Smartseq2
SS2_19_276_L3


title: mouse muscle ischemia d21 SS2_19_276_K16

description:
Smartseq2
SS2_19_276_K16


title: mouse muscle ischemia d21 SS2_19_276_K22

description:
Smartseq2
SS2_19_276_K22


title: mouse muscle ischemia d21 SS2_19_276_K19

description:
Smartseq2
SS2_19_276_K19


title: mouse muscle ischemia d21 SS2_19_276_L1

description:
Smartseq2
SS2_19_276_L1


title: mouse muscle ischemia d21 SS2_19_276_K17

description:
Smartseq2
SS2_19_276_K17


title: mouse muscle ischemia d21 SS2_19_276_K15

description:
Smartseq2
SS2_19_276_K15


title: mouse muscle ischemia d21 SS2_19_276_K14

description:
Smartseq2
SS2_19_276_K14


title: mouse muscle ischemia d21 SS2_19_276_K8

description:
Smartseq2
SS2_19_276_K8


title: mouse muscle ischemia d21 SS2_19_276_K12

description:
Smartseq2
SS2_19_276_K12


title: mouse muscle ischemia d21 SS2_19_276_K13

description:
Smartseq2
SS2_19_276_K13


title: mouse muscle ischemia d21 SS2_19_276_K20

description:
Smartseq2
SS2_19_276_K20


title: mouse muscle ischemia d21 SS2_19_276_K11

description:
Smartseq2
SS2_19_276_K11


title: mouse muscle ischemia d21 SS2_19_276_J23

description:
Smartseq2
SS2_19_276_J23


title: mouse muscle ischemia d21 SS2_19_276_J24

description:
Smartseq2
SS2_19_276_J24


title: mouse muscle ischemia d21 SS2_19_276_K10

description:
Smartseq2
SS2_19_276_K10


title: mouse muscle ischemia d21 SS2_19_276_K9

description:
Smartseq2
SS2_19_276_K9


title: mouse muscle ischemia d21 SS2_19_276_K7

description:
Smartseq2
SS2_19_276_K7


title: mouse muscle ischemia d21 SS2_19_276_K6

description:
Smartseq2
SS2_19_276_K6


title: mouse muscle ischemia d21 SS2_19_276_J22

description:
Smartseq2
SS2_19_276_J22


title: mouse muscle ischemia d21 SS2_19_276_J19

description:
Smartseq2
SS2_19_276_J19


title: mouse muscle ischemia d21 SS2_19_276_K5

description:
Smartseq2
SS2_19_276_K5


title: mouse muscle ischemia d21 SS2_19_276_K4

description:
Smartseq2
SS2_19_276_K4


title: mouse muscle ischemia d21 SS2_19_276_J18

description:
Smartseq2
SS2_19_276_J18


title: mouse muscle ischemia d21 SS2_19_276_J17

description:
Smartseq2
SS2_19_276_J17


title: mouse muscle ischemia d21 SS2_19_276_K3

description:
Smartseq2
SS2_19_276_K3


title: mouse muscle ischemia d21 SS2_19_276_K2

description:
Smartseq2
SS2_19_276_K2


title: mouse muscle ischemia d21 SS2_19_276_O11

description:
Smartseq2
SS2_19_276_O11


title: mouse muscle ischemia d21 SS2_19_276_J16

description:
Smartseq2
SS2_19_276_J16


title: mouse muscle ischemia d21 SS2_19_276_J15

description:
Smartseq2
SS2_19_276_J15


title: mouse muscle ischemia d21 SS2_19_276_K1

description:
Smartseq2
SS2_19_276_K1


title: mouse muscle ischemia d21 SS2_19_276_J20

description:
Smartseq2
SS2_19_276_J20


title: mouse muscle ischemia d21 SS2_19_276_J9

description:
Smartseq2
SS2_19_276_J9


title: mouse muscle ischemia d21 SS2_19_276_J14

description:
Smartseq2
SS2_19_276_J14


title: mouse muscle ischemia d21 SS2_19_276_J11

description:
Smartseq2
SS2_19_276_J11


title: mouse muscle ischemia d21 SS2_19_276_J12

description:
Smartseq2
SS2_19_276_J12


title: mouse muscle ischemia d21 SS2_19_276_J13

description:
Smartseq2
SS2_19_276_J13


title: mouse muscle ischemia d21 SS2_19_276_J7

description:
Smartseq2
SS2_19_276_J7


title: mouse muscle ischemia d21 SS2_19_276_J5

description:
Smartseq2
SS2_19_276_J5


title: mouse muscle ischemia d21 SS2_19_276_J8

description:
Smartseq2
SS2_19_276_J8


title: mouse muscle ischemia d21 SS2_19_276_J4

description:
Smartseq2
SS2_19_276_J4


title: mouse muscle ischemia d21 SS2_19_276_J10

description:
Smartseq2
SS2_19_276_J10


title: mouse muscle ischemia d21 SS2_19_276_J6

description:
Smartseq2
SS2_19_276_J6


title: mouse muscle ischemia d21 SS2_19_276_I23

description:
Smartseq2
SS2_19_276_I23


title: mouse muscle ischemia d21 SS2_19_276_I21

description:
Smartseq2
SS2_19_276_I21


title: mouse muscle ischemia d21 SS2_19_276_I19

description:
Smartseq2
SS2_19_276_I19


title: mouse muscle ischemia d21 SS2_19_276_I16

description:
Smartseq2
SS2_19_276_I16


title: mouse muscle ischemia d21 SS2_19_276_J3

description:
Smartseq2
SS2_19_276_J3


title: mouse muscle ischemia d21 SS2_19_276_I20

description:
Smartseq2
SS2_19_276_I20


title: mouse muscle ischemia d21 SS2_19_276_J21

description:
Smartseq2
SS2_19_276_J21


title: mouse muscle ischemia d21 SS2_19_276_I22

description:
Smartseq2
SS2_19_276_I22


title: mouse muscle ischemia d21 SS2_19_276_J1

description:
Smartseq2
SS2_19_276_J1


title: mouse muscle ischemia d21 SS2_19_276_I24

description:
Smartseq2
SS2_19_276_I24


title: mouse muscle ischemia d21 SS2_19_276_I14

description:
Smartseq2
SS2_19_276_I14


title: mouse muscle ischemia d21 SS2_19_276_I12

description:
Smartseq2
SS2_19_276_I12


title: mouse muscle ischemia d21 SS2_19_276_I10

description:
Smartseq2
SS2_19_276_I10


title: mouse muscle ischemia d21 SS2_19_276_I15

description:
Smartseq2
SS2_19_276_I15


title: mouse muscle ischemia d21 SS2_19_276_I11

description:
Smartseq2
SS2_19_276_I11


title: mouse muscle ischemia d21 SS2_19_276_I13

description:
Smartseq2
SS2_19_276_I13


title: mouse muscle ischemia d21 SS2_19_276_I9

description:
Smartseq2
SS2_19_276_I9


title: mouse muscle ischemia d21 SS2_19_276_I5

description:
Smartseq2
SS2_19_276_I5


title: mouse muscle ischemia d21 SS2_19_276_I7

description:
Smartseq2
SS2_19_276_I7


title: mouse muscle ischemia d21 SS2_19_276_J2

description:
Smartseq2
SS2_19_276_J2


title: mouse muscle ischemia d21 SS2_19_276_I6

description:
Smartseq2
SS2_19_276_I6


title: mouse muscle ischemia d21 SS2_19_276_I3

description:
Smartseq2
SS2_19_276_I3


title: mouse muscle ischemia d21 SS2_19_276_H24

description:
Smartseq2
SS2_19_276_H24


title: mouse muscle ischemia d21 SS2_19_276_I2

description:
Smartseq2
SS2_19_276_I2


title: mouse muscle ischemia d21 SS2_19_276_I18

description:
Smartseq2
SS2_19_276_I18


title: mouse muscle ischemia d21 SS2_19_276_H22

description:
Smartseq2
SS2_19_276_H22


title: mouse muscle ischemia d21 SS2_19_276_I1

description:
Smartseq2
SS2_19_276_I1


title: mouse muscle ischemia d21 SS2_19_276_H23

description:
Smartseq2
SS2_19_276_H23


title: mouse muscle ischemia d21 SS2_19_276_I17

description:
Smartseq2
SS2_19_276_I17


title: mouse muscle ischemia d21 SS2_19_276_H19

description:
Smartseq2
SS2_19_276_H19


title: mouse muscle ischemia d21 SS2_19_276_H21

description:
Smartseq2
SS2_19_276_H21


title: mouse muscle ischemia d21 SS2_19_276_H16

description:
Smartseq2
SS2_19_276_H16


title: mouse muscle ischemia d21 SS2_19_276_H15

description:
Smartseq2
SS2_19_276_H15


title: mouse muscle ischemia d21 SS2_19_276_H18

description:
Smartseq2
SS2_19_276_H18


title: mouse muscle ischemia d21 SS2_19_276_H13

description:
Smartseq2
SS2_19_276_H13


title: mouse muscle ischemia d21 SS2_19_276_H12

description:
Smartseq2
SS2_19_276_H12


title: mouse muscle ischemia d21 SS2_19_276_H20

description:
Smartseq2
SS2_19_276_H20


title: mouse muscle ischemia d21 SS2_19_276_H10

description:
Smartseq2
SS2_19_276_H10


title: mouse muscle ischemia d21 SS2_19_276_I8

description:
Smartseq2
SS2_19_276_I8


title: mouse muscle ischemia d21 SS2_19_276_H11

description:
Smartseq2
SS2_19_276_H11


title: mouse muscle ischemia d21 SS2_19_276_I4

description:
Smartseq2
SS2_19_276_I4


title: mouse muscle ischemia d21 SS2_19_276_H17

description:
Smartseq2
SS2_19_276_H17


title: mouse muscle ischemia d21 SS2_19_276_H7

description:
Smartseq2
SS2_19_276_H7


title: mouse muscle ischemia d21 SS2_19_276_H9

description:
Smartseq2
SS2_19_276_H9


title: mouse muscle ischemia d21 SS2_19_276_H8

description:
Smartseq2
SS2_19_276_H8


title: mouse muscle ischemia d21 SS2_19_276_H3

description:
Smartseq2
SS2_19_276_H3


title: mouse muscle ischemia d21 SS2_19_276_H4

description:
Smartseq2
SS2_19_276_H4


title: mouse muscle ischemia d21 SS2_19_276_H2

description:
Smartseq2
SS2_19_276_H2


title: mouse muscle ischemia d21 SS2_19_276_H6

description:
Smartseq2
SS2_19_276_H6


title: mouse muscle ischemia d21 SS2_19_276_H5

description:
Smartseq2
SS2_19_276_H5


title: mouse muscle ischemia d21 SS2_19_276_G20

description:
Smartseq2
SS2_19_276_G20


title: mouse muscle ischemia d21 SS2_19_276_G19

description:
Smartseq2
SS2_19_276_G19


title: mouse muscle ischemia d21 SS2_19_276_G18

description:
Smartseq2
SS2_19_276_G18


title: mouse muscle ischemia d21 SS2_19_276_G24

description:
Smartseq2
SS2_19_276_G24


title: mouse muscle ischemia d21 SS2_19_276_G23

description:
Smartseq2
SS2_19_276_G23


title: mouse muscle ischemia d21 SS2_19_276_G22

description:
Smartseq2
SS2_19_276_G22


title: mouse muscle ischemia d21 SS2_19_276_G15

description:
Smartseq2
SS2_19_276_G15


title: mouse muscle ischemia d21 SS2_19_276_G21

description:
Smartseq2
SS2_19_276_G21


title: mouse muscle ischemia d21 SS2_19_276_G17

description:
Smartseq2
SS2_19_276_G17


title: mouse muscle ischemia d21 SS2_19_276_G16

description:
Smartseq2
SS2_19_276_G16


title: mouse muscle ischemia d21 SS2_19_276_G11

description:
Smartseq2
SS2_19_276_G11


title: mouse muscle ischemia d21 SS2_19_276_G10

description:
Smartseq2
SS2_19_276_G10


title: mouse muscle ischemia d21 SS2_19_276_G6

description:
Smartseq2
SS2_19_276_G6


title: mouse muscle ischemia d21 SS2_19_276_H14

description:
Smartseq2
SS2_19_276_H14


title: mouse muscle ischemia d21 SS2_19_276_G14

description:
Smartseq2
SS2_19_276_G14


title: mouse muscle ischemia d21 SS2_19_276_G13

description:
Smartseq2
SS2_19_276_G13


title: mouse muscle ischemia d21 SS2_19_276_G3

description:
Smartseq2
SS2_19_276_G3


title: mouse muscle ischemia d21 SS2_19_276_H1

description:
Smartseq2
SS2_19_276_H1


title: mouse muscle ischemia d21 SS2_19_276_G12

description:
Smartseq2
SS2_19_276_G12


title: mouse muscle ischemia d21 SS2_19_276_G8

description:
Smartseq2
SS2_19_276_G8


title: mouse muscle ischemia d21 SS2_19_276_G2

description:
Smartseq2
SS2_19_276_G2


title: mouse muscle ischemia d21 SS2_19_276_G7

description:
Smartseq2
SS2_19_276_G7


title: mouse muscle ischemia d21 SS2_19_276_G1

description:
Smartseq2
SS2_19_276_G1


title: mouse muscle ischemia d21 SS2_19_276_F24

description:
Smartseq2
SS2_19_276_F24


title: mouse muscle ischemia d21 SS2_19_276_F22

description:
Smartseq2
SS2_19_276_F22


title: mouse muscle ischemia d21 SS2_19_276_F23

description:
Smartseq2
SS2_19_276_F23


title: mouse muscle ischemia d21 SS2_19_276_F19

description:
Smartseq2
SS2_19_276_F19


title: mouse muscle ischemia d21 SS2_19_276_F18

description:
Smartseq2
SS2_19_276_F18


title: mouse muscle ischemia d21 SS2_19_276_F17

description:
Smartseq2
SS2_19_276_F17


title: mouse muscle ischemia d21 SS2_19_276_F20

description:
Smartseq2
SS2_19_276_F20


title: mouse muscle ischemia d21 SS2_19_276_F15

description:
Smartseq2
SS2_19_276_F15


title: mouse muscle ischemia d21 SS2_19_276_F14

description:
Smartseq2
SS2_19_276_F14


title: mouse muscle ischemia d21 SS2_19_276_F21

description:
Smartseq2
SS2_19_276_F21


title: mouse muscle ischemia d21 SS2_19_276_G9

description:
Smartseq2
SS2_19_276_G9


title: mouse muscle ischemia d21 SS2_19_276_G5

description:
Smartseq2
SS2_19_276_G5


title: mouse muscle ischemia d21 SS2_19_276_F12

description:
Smartseq2
SS2_19_276_F12


title: mouse muscle ischemia d21 SS2_19_276_F13

description:
Smartseq2
SS2_19_276_F13


title: mouse muscle ischemia d21 SS2_19_276_F16

description:
Smartseq2
SS2_19_276_F16


title: mouse muscle ischemia d21 SS2_19_276_F9

description:
Smartseq2
SS2_19_276_F9


title: mouse muscle ischemia d21 SS2_19_276_F11

description:
Smartseq2
SS2_19_276_F11


title: mouse muscle ischemia d21 SS2_19_276_F10

description:
Smartseq2
SS2_19_276_F10


title: mouse muscle ischemia d21 SS2_19_276_F6

description:
Smartseq2
SS2_19_276_F6


title: mouse muscle ischemia d21 SS2_19_276_E19

description:
Smartseq2
SS2_19_276_E19


title: mouse muscle ischemia d21 SS2_19_276_E22

description:
Smartseq2
SS2_19_276_E22


title: mouse muscle ischemia d21 SS2_19_276_F1

description:
Smartseq2
SS2_19_276_F1


title: mouse muscle ischemia d21 SS2_19_276_G4

description:
Smartseq2
SS2_19_276_G4


title: mouse muscle ischemia d21 SS2_19_276_F8

description:
Smartseq2
SS2_19_276_F8


title: mouse muscle ischemia d21 SS2_19_276_F7

description:
Smartseq2
SS2_19_276_F7


title: mouse muscle ischemia d21 SS2_19_276_E14

description:
Smartseq2
SS2_19_276_E14


title: mouse muscle ischemia d21 SS2_19_276_F5

description:
Smartseq2
SS2_19_276_F5


title: mouse muscle ischemia d21 SS2_19_276_E8

description:
Smartseq2
SS2_19_276_E8


title: mouse muscle ischemia d21 SS2_19_276_E10

description:
Smartseq2
SS2_19_276_E10


title: mouse muscle ischemia d21 SS2_19_276_F4

description:
Smartseq2
SS2_19_276_F4


title: mouse muscle ischemia d21 SS2_19_276_E5

description:
Smartseq2
SS2_19_276_E5


title: mouse muscle ischemia d21 SS2_19_276_F3

description:
Smartseq2
SS2_19_276_F3


title: mouse muscle ischemia d21 SS2_19_276_F2

description:
Smartseq2
SS2_19_276_F2


title: mouse muscle ischemia d21 SS2_19_276_E3

description:
Smartseq2
SS2_19_276_E3


title: mouse muscle ischemia d21 SS2_19_276_E24

description:
Smartseq2
SS2_19_276_E24


title: mouse muscle ischemia d21 SS2_19_276_E21

description:
Smartseq2
SS2_19_276_E21


title: mouse muscle ischemia d21 SS2_19_276_E23

description:
Smartseq2
SS2_19_276_E23


title: mouse muscle ischemia d21 SS2_19_276_E1

description:
Smartseq2
SS2_19_276_E1


title: mouse muscle ischemia d21 SS2_19_276_D23

description:
Smartseq2
SS2_19_276_D23


title: mouse muscle ischemia d21 SS2_19_276_D24

description:
Smartseq2
SS2_19_276_D24


title: mouse muscle ischemia d21 SS2_19_276_E20

description:
Smartseq2
SS2_19_276_E20


title: mouse muscle ischemia d21 SS2_19_276_E18

description:
Smartseq2
SS2_19_276_E18


title: mouse muscle ischemia d21 SS2_19_276_D21

description:
Smartseq2
SS2_19_276_D21


title: mouse muscle ischemia d21 SS2_19_276_E17

description:
Smartseq2
SS2_19_276_E17


title: mouse muscle ischemia d21 SS2_19_276_E15

description:
Smartseq2
SS2_19_276_E15


title: mouse muscle ischemia d21 SS2_19_276_E7

description:
Smartseq2
SS2_19_276_E7


title: mouse muscle ischemia d21 SS2_19_276_E13

description:
Smartseq2
SS2_19_276_E13


title: mouse muscle ischemia d21 SS2_19_276_D17

description:
Smartseq2
SS2_19_276_D17


title: mouse muscle ischemia d21 SS2_19_276_E6

description:
Smartseq2
SS2_19_276_E6


title: mouse muscle ischemia d21 SS2_19_276_D18

description:
Smartseq2
SS2_19_276_D18


title: mouse muscle ischemia d21 SS2_19_276_E12

description:
Smartseq2
SS2_19_276_E12


title: mouse muscle ischemia d21 SS2_19_276_E11

description:
Smartseq2
SS2_19_276_E11


title: mouse muscle ischemia d21 SS2_19_276_E2

description:
Smartseq2
SS2_19_276_E2


title: mouse muscle ischemia d21 SS2_19_276_D15

description:
Smartseq2
SS2_19_276_D15


title: mouse muscle ischemia d21 SS2_19_276_E16

description:
Smartseq2
SS2_19_276_E16


title: mouse muscle ischemia d21 SS2_19_276_E4

description:
Smartseq2
SS2_19_276_E4


title: mouse muscle ischemia d21 SS2_19_276_D22

description:
Smartseq2
SS2_19_276_D22


title: mouse muscle ischemia d21 SS2_19_276_D8

description:
Smartseq2
SS2_19_276_D8


title: mouse muscle ischemia d21 SS2_19_276_D6

description:
Smartseq2
SS2_19_276_D6


title: mouse muscle ischemia d21 SS2_19_276_E9

description:
Smartseq2
SS2_19_276_E9


title: mouse muscle ischemia d21 SS2_19_276_D7

description:
Smartseq2
SS2_19_276_D7


title: mouse muscle ischemia d21 SS2_19_276_D4

description:
Smartseq2
SS2_19_276_D4


title: mouse muscle ischemia d21 SS2_19_276_D12

description:
Smartseq2
SS2_19_276_D12


title: mouse muscle ischemia d21 SS2_19_276_D20

description:
Smartseq2
SS2_19_276_D20


title: mouse muscle ischemia d21 SS2_19_276_D11

description:
Smartseq2
SS2_19_276_D11


title: mouse muscle ischemia d21 SS2_19_276_D14

description:
Smartseq2
SS2_19_276_D14


title: mouse muscle ischemia d21 SS2_19_276_D3

description:
Smartseq2
SS2_19_276_D3


title: mouse muscle ischemia d21 SS2_19_276_D5

description:
Smartseq2
SS2_19_276_D5


title: mouse muscle ischemia d21 SS2_19_276_D16

description:
Smartseq2
SS2_19_276_D16


title: mouse muscle ischemia d21 SS2_19_276_D2

description:
Smartseq2
SS2_19_276_D2


title: mouse muscle ischemia d21 SS2_19_276_C22

description:
Smartseq2
SS2_19_276_C22


title: mouse muscle ischemia d21 SS2_19_276_C18

description:
Smartseq2
SS2_19_276_C18


title: mouse muscle ischemia d21 SS2_19_276_D19

description:
Smartseq2
SS2_19_276_D19


title: mouse muscle ischemia d21 SS2_19_276_D1

description:
Smartseq2
SS2_19_276_D1


title: mouse muscle ischemia d21 SS2_19_276_D9

description:
Smartseq2
SS2_19_276_D9


title: mouse muscle ischemia d21 SS2_19_276_C17

description:
Smartseq2
SS2_19_276_C17


title: mouse muscle ischemia d21 SS2_19_276_C15

description:
Smartseq2
SS2_19_276_C15


title: mouse muscle ischemia d21 SS2_19_276_C14

description:
Smartseq2
SS2_19_276_C14


title: mouse muscle ischemia d21 SS2_19_276_C23

description:
Smartseq2
SS2_19_276_C23


title: mouse muscle ischemia d21 SS2_19_276_C24

description:
Smartseq2
SS2_19_276_C24


title: mouse muscle ischemia d21 SS2_19_276_D13

description:
Smartseq2
SS2_19_276_D13


title: mouse muscle ischemia d21 SS2_19_276_C20

description:
Smartseq2
SS2_19_276_C20


title: mouse muscle ischemia d21 SS2_19_276_D10

description:
Smartseq2
SS2_19_276_D10


title: mouse muscle ischemia d21 SS2_19_276_C21

description:
Smartseq2
SS2_19_276_C21


title: mouse muscle ischemia d21 SS2_19_276_C9

description:
Smartseq2
SS2_19_276_C9


title: mouse muscle ischemia d21 SS2_19_276_C16

description:
Smartseq2
SS2_19_276_C16


title: mouse muscle ischemia d21 SS2_19_276_C13

description:
Smartseq2
SS2_19_276_C13


title: mouse muscle ischemia d21 SS2_19_276_C6

description:
Smartseq2
SS2_19_276_C6


title: mouse muscle ischemia d21 SS2_19_276_C12

description:
Smartseq2
SS2_19_276_C12


title: mouse muscle ischemia d21 SS2_19_276_C11

description:
Smartseq2
SS2_19_276_C11


title: mouse muscle ischemia d21 SS2_19_276_C19

description:
Smartseq2
SS2_19_276_C19


title: mouse muscle ischemia d21 SS2_19_276_C8

description:
Smartseq2
SS2_19_276_C8


title: mouse muscle ischemia d21 SS2_19_276_C10

description:
Smartseq2
SS2_19_276_C10


title: mouse muscle ischemia d21 SS2_19_276_C3

description:
Smartseq2
SS2_19_276_C3


title: mouse muscle ischemia d21 SS2_19_276_C1

description:
Smartseq2
SS2_19_276_C1


title: mouse muscle ischemia d21 SS2_19_276_C5

description:
Smartseq2
SS2_19_276_C5


title: mouse muscle ischemia d21 SS2_19_276_B17

description:
Smartseq2
SS2_19_276_B17


title: mouse muscle ischemia d21 SS2_19_276_C4

description:
Smartseq2
SS2_19_276_C4


title: mouse muscle ischemia d21 SS2_19_276_C7

description:
Smartseq2
SS2_19_276_C7


title: mouse muscle ischemia d21 SS2_19_276_C2

description:
Smartseq2
SS2_19_276_C2


title: mouse muscle ischemia d21 SS2_19_276_B24

description:
Smartseq2
SS2_19_276_B24


title: mouse muscle ischemia d21 SS2_19_276_B23

description:
Smartseq2
SS2_19_276_B23


title: mouse muscle ischemia d21 SS2_19_276_B22

description:
Smartseq2
SS2_19_276_B22


title: mouse muscle ischemia d21 SS2_19_276_B21

description:
Smartseq2
SS2_19_276_B21


title: mouse muscle ischemia d21 SS2_19_276_B6

description:
Smartseq2
SS2_19_276_B6


title: mouse muscle ischemia d21 SS2_19_276_B5

description:
Smartseq2
SS2_19_276_B5


title: mouse muscle ischemia d21 SS2_19_276_B20

description:
Smartseq2
SS2_19_276_B20


title: mouse muscle ischemia d21 SS2_19_276_A24

description:
Smartseq2
SS2_19_276_A24


title: mouse muscle ischemia d21 SS2_19_276_B1

description:
Smartseq2
SS2_19_276_B1


title: mouse muscle ischemia d21 SS2_19_276_B2

description:
Smartseq2
SS2_19_276_B2


title: mouse muscle ischemia d21 SS2_19_276_B16

description:
Smartseq2
SS2_19_276_B16


title: mouse muscle ischemia d21 SS2_19_276_B19

description:
Smartseq2
SS2_19_276_B19


title: mouse muscle ischemia d21 SS2_19_276_A21

description:
Smartseq2
SS2_19_276_A21


title: mouse muscle ischemia d21 SS2_19_276_A19

description:
Smartseq2
SS2_19_276_A19


title: mouse muscle ischemia d21 SS2_19_276_B18

description:
Smartseq2
SS2_19_276_B18


title: mouse muscle ischemia d21 SS2_19_276_A17

description:
Smartseq2
SS2_19_276_A17


title: mouse muscle ischemia d21 SS2_19_276_A16

description:
Smartseq2
SS2_19_276_A16


title: mouse muscle ischemia d21 SS2_19_276_A15

description:
Smartseq2
SS2_19_276_A15


title: mouse muscle ischemia d21 SS2_19_276_A14

description:
Smartseq2
SS2_19_276_A14


title: mouse muscle ischemia d21 SS2_19_276_A13

description:
Smartseq2
SS2_19_276_A13


title: mouse muscle ischemia d21 SS2_19_276_A12

description:
Smartseq2
SS2_19_276_A12


title: mouse muscle ischemia d21 SS2_19_276_A22

description:
Smartseq2
SS2_19_276_A22


title: mouse muscle ischemia d21 SS2_19_276_B15

description:
Smartseq2
SS2_19_276_B15


title: mouse muscle ischemia d21 SS2_19_276_A10

description:
Smartseq2
SS2_19_276_A10


title: mouse muscle ischemia d21 SS2_19_276_A6

description:
Smartseq2
SS2_19_276_A6


title: mouse muscle ischemia d21 SS2_19_276_B14

description:
Smartseq2
SS2_19_276_B14


title: mouse muscle ischemia d21 SS2_19_276_B12

description:
Smartseq2
SS2_19_276_B12


title: mouse muscle ischemia d21 SS2_19_276_B11

description:
Smartseq2
SS2_19_276_B11


title: mouse muscle ischemia d21 SS2_19_276_B13

description:
Smartseq2
SS2_19_276_B13


title: mouse muscle ischemia d21 SS2_19_276_B10

description:
Smartseq2
SS2_19_276_B10


title: mouse muscle ischemia d21 SS2_19_276_B9

description:
Smartseq2
SS2_19_276_B9


title: mouse muscle ischemia d21 SS2_19_276_B8

description:
Smartseq2
SS2_19_276_B8


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep6

type: RNA

city: Baltimore

first: Apurva

last: Borcar

state: MD

address: 685 W. Baltimore Street, MSTF 5-34

department: Anesthesiology

country: USA

institute: University of Maryland School of Medicine

hyb_protocol: ss-cDNA was fragmented and labeled before hybridization onto the microarray chips, which were washed and processed using an Affymetrix GeneChip system 3000 7G.

scan_protocol: Affymetrix image data (.CEL files) was further analyzed using the R statistical analysis tool. The R ‘oligo' package was used to access the intensity values which were normalized using the ‘Robust Multichip Average (RMA)’ normalization method provided by the R ’limma’ package.

data_processing:
The samples were assessed and corrected for any batch effects before downstream analyses. Principal component analysis was utilized to identify and exclude any outlier samples. A general linear model was utilized to fit the expression values for each gene.
TXT files are available along with the CEL files. TXT files compared treatment groups to the control group after outliers were removed. The list of .TXT files and associated .CEL files are found on the Matrix table. We used the analyzed data within TXT files for our results and conclusions.

label: Biotin

organism: Rattus norvegicus

source_name: Blood

label_protocol: 150 ng RNA was transcribed to double-stranded cDNA, followed by synthesis and purification of cRNA. 2nd-cycle ss-cDNA was then synthesized and then purified after RNA hydrolysis using RNase H.

growth_protocol: Rats were subjected to different levels of hypobaria and/or hyperoxia for different durations of time at room temp. Immediately after "flight", rats were anesthetized and euthanized and tissue was collected.

extract_protocol: All tissues were processed for RNA via commercially available and appropriate kits (trizol for solid tissue, PAXgene kit for blood).

treatment_protocol: Heart, lung, and hippocampus samples were placed on dry ice immediately. Blood was collected in PAXgene blood RNA stabilization tubes and frozen. Solid tissues were placed in RNAlater ICE before processing.

value: Blood


title: mouse muscle ischemia d21 SS2_19_276_A1

description:
Smartseq2
SS2_19_276_A1


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep5


title: mouse muscle ischemia d21 SS2_19_276_B7

description:
Smartseq2
SS2_19_276_B7


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep5


title: mouse muscle ischemia d21 SS2_19_276_B4

description:
Smartseq2
SS2_19_276_B4


title: mouse muscle ischemia d21 SS2_19_276_B3

description:
Smartseq2
SS2_19_276_B3


title: Blood of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep4

description: Identified as an outlier via PCA and therefore excluded from subsequent analysis.


title: mouse muscle ischemia d21 SS2_19_276_A23

description:
Smartseq2
SS2_19_276_A23


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep6


title: Blood of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep3


title: mouse muscle ischemia d21 SS2_19_276_A20

description:
Smartseq2
SS2_19_276_A20


title: Blood of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep5


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep6

description: These were the control group animals, therefore they were used as reference for differential expression of the treated groups and do not have a separate processed data file.


title: mouse muscle ischemia d21 SS2_19_276_A18

description:
Smartseq2
SS2_19_276_A18


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep4


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep3


title: mouse muscle ischemia d21 SS2_19_276_A11

description:
Smartseq2
SS2_19_276_A11


title: mouse muscle ischemia d21 SS2_19_276_A9

description:
Smartseq2
SS2_19_276_A9


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep4


title: mouse muscle ischemia d21 SS2_19_276_A8

description:
Smartseq2
SS2_19_276_A8


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep3


title: mouse muscle ischemia d21 SS2_19_276_A7

description:
Smartseq2
SS2_19_276_A7


title: mouse muscle ischemia d21 SS2_19_276_A3

description:
Smartseq2
SS2_19_276_A3


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep4


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep1


title: Blood of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep4


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep6


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep5


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep6


title: Blood of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep3


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep6


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep5


title: Blood of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep5


title: mouse muscle ischemia d21 SS2_19_276_A4

description:
Smartseq2
SS2_19_276_A4


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep5


title: Blood of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep5


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep5


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep4


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep3


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep3


title: Blood of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep4


title: Blood of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep2


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep2


title: Blood of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep1


title: Blood of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep3


title: Blood of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep2


title: Blood of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep2


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep6

source_name: Heart

value: Heart


title: Blood of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep3


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep2


title: Blood of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep1


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep6


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep3


title: Blood of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep3


title: Blood of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep1


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep1


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep6


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep5


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep5


title: Blood of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep4


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep3


title: Blood of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep4


title: mouse muscle ischemia d21 SS2_19_276_A5

description:
Smartseq2
SS2_19_276_A5


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep1


title: DJH-INV-VkRSS-JkRSS_v-Abl_untreated_JH4_rep3

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital / Harvard Medical School

description: aligned to mm9_DQ52JH4_VkRSS genome

library_source: genomic

data_processing:
Standard basecalling formats for Miseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp
Assembly: mm9 genome, AJ851868/mm9 hybrid genome and indicated custom genomes
Supplementary files format and content: Tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paired end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: HTGTS-V(D)J-seq

molecule: genomic DNA

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl cell lines were cultured in RPMI1640 media with 15% FBS

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.2% SDS, 10mM Tris-HCl pH7.4, 2mM EDTA pH8.0, 200ug/ml proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.4, 0.5mM EDTA pH8.0
HTGTS-V(D)J-seq libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primers

treatment_protocol:
Pre-B cells were isolated from mouse bone marrow by FACS sorting for B220+ CD43low IgM- cells
RAG complementation was performed by infecting v-Abl cell lines with RAG1 and/or RAG2 retrovirus followed by selection with blasticidin or puromycin
G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days
WAPL-depletion was performed by treating WAPL-degron v-Abl cell lines with 150uM IAA and 2mg/ml Dox for 3 days, starting on day 1 of G1-arrest

tag: cell line

value: v-Abl transformed pro-B cell line

tag: strain

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-INV-VkRSS-JkRSS

value: RAG1&2 complementation, G1-arrest, untreated


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep6


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep5


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep5


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep6


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep1


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep6


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep3


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep2


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep6


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep6

description: aligned to mm9AJ_DQ52uptoVkRSS genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-D-VkRSS

value: RAG2 complementation, G1-arrest


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep1


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep4


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep5

description: aligned to mm9AJ_DQ52uptoVkRSS genome


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep6


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep6


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep3


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep2


title: Igh-Igk-hybrid-D_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-D


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep2


title: Igh-Igk-hybrid-D_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: mouse muscle ischemia d21 SS2_19_276_A2

description:
Smartseq2
SS2_19_276_A2


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep2


title: Heart of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep1


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep5


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep3


title: Heart of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep2


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep6


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep2


title: DJH-INV-VkRSS-JkRSS_v-Abl_untreated_JH4_rep2

description: aligned to mm9_DQ52JH4_VkRSS genome


title: DJH-INV-VkRSS-JkRSS_v-Abl_untreated_JH4_rep1

description: aligned to mm9_DQ52JH4_VkRSS genome


title: Heart of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep2


title: single-Jk5-PKO_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-PKO


title: single-Jk5-PKO_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: DJH-INV-VkRSS_v-Abl_untreated_JH4_rep4

description: aligned to mm9_DQ52JH4_VkRSS genome

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-INV-VkRSS


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep4


title: DJH-INV-VkRSS_v-Abl_untreated_JH4_rep3

description: aligned to mm9_DQ52JH4_VkRSS genome


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep3


title: DJH-INV-VkRSS_v-Abl_untreated_JH4_rep1

description: aligned to mm9_DQ52JH4_VkRSS genome


title: DJH-INV-VkRSS_v-Abl_untreated_JH4_rep2

description: aligned to mm9_DQ52JH4_VkRSS genome


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep1


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep3


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep4

description: aligned to mm9AJ_DQ52uptoVkRSS genome


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep3

description: aligned to mm9AJ_DQ52uptoVkRSS genome


title: Heart of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep1


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep2


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep2

description: aligned to mm9AJ_DQ52uptoVkRSS genome


title: single-Jk5-single-Igh_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-single Igh


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep4


title: single-Jk5-single-Igh_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: single-Jk5-single-Igh_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep3


title: Igh-Igk-hybrid-D_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: Heart of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep1


title: Igh-Igk-hybrid-D-VkRSS_v-Abl_Jk5_rep1

description: aligned to mm9AJ_DQ52uptoVkRSS genome


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep4


title: Igh-Igk-hybrid-D_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep4


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep3


title: single-Jk5-PKO_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: Igh-Igk-hybrid-Vk-JkRSS_v-Abl_JH1_rep3

description: aligned to mm9AJ_JH1toJk5RSS genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-Vk-JkRSS


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep3


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep3


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep2


title: Heart of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep1


title: Igh-Igk-hybrid-Vk-JkRSS_v-Abl_JH1_rep1

description: aligned to mm9AJ_JH1toJk5RSS genome


title: Igh-Igk-hybrid-Vk_v-Abl_JH1_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-Vk


title: Igh-Igk-hybrid-Vk-JkRSS-PKO_v-Abl_JH1_rep3

description: aligned to mm9AJ_JH1toJk5RSS genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-Vk-JkRSS-PKO


title: Igh-Igk-hybrid-Vk-JkRSS-PKO_v-Abl_JH1_rep2

description: aligned to mm9AJ_JH1toJk5RSS genome


title: Heart of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep1


title: Igh-Igk-hybrid-Vk-JkRSS-PKO_v-Abl_JH1_rep1

description: aligned to mm9AJ_JH1toJk5RSS genome


title: Igh-Igk-hybrid-Vk_v-Abl_JH1_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: single-Jk5-single-Igh-JHRSS_v-Abl_Jk5_rep3

description: aligned to mm9AJ_Jk5toJH1RSS genome

value: Rag2-/-, Emu-Bcl2, single Jk5-single Igh-JHRSS


title: single-Jk5-single-Igh-JHRSS_v-Abl_Jk5_rep2

description: aligned to mm9AJ_Jk5toJH1RSS genome


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep6

source_name: Lung

value: Lung


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep4


title: iPS_C5

city: Solna

first: Anna

last: Herland

address: Tomtebodagatan 23

institute: SciLifelab KTH

library_source: transcriptomic

data_processing:
The base calling and demultiplexing of the paired-end reads were performed using Illumina bcl2fastq (v2.20).
The adapter trimming was done using BBMAP (v38.41).
The sequence data quality was then assessed using FastQC (v0.11.8).
The reads were then aligned to the Ensembl GRCh38 reference genome using STAR (v2.6.1d).
The gene counts were estimated using featureCounts (v1.5.1). The count data was then imported into the Bioconductor package DESeq2 (V1.34) to test for differential expression using Wald tests.
Assembly: Ensembl GRCh38
Supplementary files format and content: The csv file contains comma separated values for raw counts and normalized counts from each run.

organism: Homo sapiens

source_name: induced pluripotent stem cell

growth_protocol: The isolated reprogrammed cells were expanded in E8 on a 6-well plate coated with 5 μg/ml of LN 521in DPBS +/+ and the isolated NSCs were expanded in N2B27 propagation media.

extract_protocol:
Total RNA was extracted from the cells using a Qiagen RNeasy Mini Kit. The initial RNA quality and concentrations were analyzed using Agilent Tapestation per the manufacturer’s instructions.
The libraries suitable for Illumina sequencing were prepared using Illumina Stranded mRNA prep ligation sample preparation protocol with a starting concentration of about 200 ng of total RNA.

treatment_protocol:
The reprogramming was performed using StemRNA 3rd Gen Reprogramming Kit (Stemgent).
Dual-SMAD inhibition protocol for neural induction.

tag: cell type

value: induced pluripotent stem cell

value: WT

value: Sendai Virus reprogramming


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep6


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep5


title: single-Jk5-single-Igh-JHRSS_v-Abl_Jk5_rep1

description: aligned to mm9AJ_Jk5toJH1RSS genome

value: v-Abl transformed pro-B cell line


title: iPS_10

value: mRNA reprogramming


title: iPS_C14


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep5


title: Heart of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep1

value: Heart


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep5


title: Heart of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep2


title: Igh-Igk-hybrid-Vk-JkRSS_v-Abl_JH1_rep2

description: aligned to mm9AJ_JH1toJk5RSS genome


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep5


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep6


title: Igh-Igk-hybrid-Vk_v-Abl_JH1_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep5


title: iPS_KTH_01


title: DJH-WT_v-Abl_WAPL-depleted_JH4_rep3

description: aligned to mm9_DQ52JH4 genome

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-WT

value: RAG1&2 complementation, G1-arrest, WAPL-depletion


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep5


title: ips_KTH_04_well


title: ips_KTH_04_chip


title: iPS_C9

value: mRNA/Sendai Virus reprogramming


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep5


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep6


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep6


title: NES_C14

source_name: neuroepithelial stem cell generated from iPSCs

value: dual-SMAD inhibition


title: NES_10

value: neuroepithelial stem cell generated from iPSCs


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep6


title: ips_KTH_06_chip


title: ips_KTH_06_well


title: ips_KTH_05_chip


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep5


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep6


title: NSC_KTH_01_chip_p6

source_name: neural stem cell generated from iPSCs

value: neural stem cell generated from iPSCs


title: ips_KTH_05_well


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep5


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep6


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep6


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep2


title: NSC_C5_chip_p6


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep1


title: NSC_C5_chip_p0


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep5


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep6


title: NES_C9


title: NSC_C5_well_p6


title: NSC_KTH_01_chip_p0


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep2


title: NSC_C9_well_p6


title: NSC_KTH_01_well_p6


title: NSC_C9_well_p0


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep3


title: NSC_KTH_01_well_p0


title: Keratinocytes, siLINC00941, MTA2-IP, rep2

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

data_processing:
reads were mapped to the reference genome (GRCh38) using bowtie2 (version v2.4.4). The following options were used to optimize the alignment process: --very-sensitive-local,  --no-discordant, --no-mix, --dovetail.
Aligned reads were filtered for MAPQ >= 30 using samtools (Li et al, 2009). Reads mapping to blacklisted genomic regions (Encode accession: ENCFF356LFX) were removed using bedtools
Peak calling was executed on all samples relative to input samples using the MACS2 software (Zhang et al, 2008). The specific options used for this analysis were as follows: -f BAMPE, -g 2.7e9, --keep-dup auto. Following peak calling, the resultant peaks were filtered based on a log q-value threshold > 20 for subsequent analyses.
Assembly: GRCh38
Supplementary files format and content: Bigwigs tracks were generated usingbamCoverage from deeptools package
Supplementary files format and content: bed file containing called MTA2 binding sites

source_name: skin

growth_protocol: Primary keratinocytes were grown to a confluency of about 80%

extract_protocol:
Cells were fixed using 1% formaldehyde at RT for 10 min, the reaction was quenched with 125 mM glycine at RT for 5 min. Cells were pelleted and then lysed in Swelling buffer (100 mM Tris, pH 7.5, 10 mM potassium acetate, 15 mM magnesium acetate, 1% Igepal, 1x cOmplete Protease Inhibitor Cocktail (Roche) and 1 mM AEBSF). Chromatin fragmentation was subsequently performed in RIPA buffer for 30 min using the S220 Focused-ultrasonicator (Covaris) in the Freq sweeping mode, intensity 8, 20% duty cycle and 200 cycles per burst. 100 µg fragmented chromatin underwent IP with 5 µg α-MTA2 antibody (Abcam, ab8106) for 16 h at 4 °C. 40 µl Protein G Dynabeads (Invitrogen) were added to the IP and incubated for 45 min at RT. The beads were washed three times with Wash buffer (100 mM Tris, pH 9.0, 0.5 M lithium chloride, 1% Igepal, 1% sodium deoxycholate and 1 mM AEBSF) followed by the elution with Elution buffer (50 mM sodium bicarbonate and 1% SDS). For reverse cross-linking, 0.2 M sodium chloride was added, and the chromatin incubated at 67 °C for 4 h following a purification step with the QIAquick PCR Purification kit (Qiagen)
NEBNext Ultra II DNA Library Preparation kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) was used following the manufacturer’s instructions

value: skin

value: Keratinocytes

tag: chip antibody

value: MTA2 (Abcam, ab8106)


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep4


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep4


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep1


title: NSC_C5_well_p0


title: Keratinocytes, siLINC00941, input, rep2


title: Lung of rat exposed to 100% oxygen at 4000 ft for 10 h, biological rep4


title: NSC_C9_chip_p6


title: Keratinocytes, siLINC00941, MTA2-IP, rep3


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep2


title: Keratinocytes, siCtrl, MTA2-IP, rep3


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep1


title: Keratinocytes, siCtrl, MTA2-IP, rep1


title: Lung of rat exposed to 100% oxygen at 0 ft for 10 h, biological rep3


title: Keratinocytes, siCtrl, MTA2-IP, rep2


title: Keratinocytes, siCtrl, input, rep2


title: Keratinocytes, siLINC00941, MTA2-IP, rep1


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep3


title: Lung of rat exposed to 21% oxygen at 4000 ft for 10 h, biological rep3


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep2


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep1


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep3


title: NSC_C9_chip_p0


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep2


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep4


title: Keratinocytes, siLINC00941, input, rep1


title: skeletal muscle wt 2306 biol rep 02

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed in two rounds using fastx-toolkit version 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit) and cutadapt version 1.8.3 (31). First, 4 random bases were trimmed from left side: fastx_trimmer -f 5 -i {INP}.fastq -o {TMP}.fastq
Next, NEXTflex adapters were trimmed. Additionally, the N-nucleotides on ends of reads were trimmed and reads containing more than 10% of the N-nucleotides were discarded: cutadapt --format="fastq" --front=”GTTCAGAGTTCTACAGTCCGACGATCNNNN” --adapter=”NNNNTGGAATTCTCGGGTGCCAAGG” --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output=”${TRIMMED}.fastq" --trim-n --match-read-wildcards ${TMP}.fastq
Trimmed reads were mapped to the mouse (mm10) genome with added pCag-EGFP MosIR sequence with following parameters: STAR --readFilesIn ${TRIMMED}.fastq.gz --runThreadN 4 --genomeDir ${GENOME_INDEX} --genomeLoad LoadAndRemove --readFilesCommand unpigz -c --readStrand Unstranded --limitBAMsortRAM 20000000000 --outFileNamePrefix ${FILENAME} --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 99999 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v4 from UCSC: genomeCoverageBed -ibam ${FILENAME}.bam -bg -split > ${FILENAME}.bedGraph wigToBigWig ${FILENAME}.bedGraph chrNameLength.txt ${FILENAME}.bw
Assembly: mm10
Supplementary files format and content: coverage genome browser tracks files: - bigWig format - generated in a non-stranded mode - not normalized for library size

source_name: skeletal muscle

extract_protocol:
Organs from adult mice (9-13 w) were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by phenol–chloroform extraction according to the manufacturer's protocol.
Small-RNA libraries were prepared using the NextFlex Small-RNA-seq v3 kit (Amplicon) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 140-160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform

value: skeletal muscle

value: Dicerwt/wt

tag: age

value: adult

tag: experiment month_year

tag: replicate


title: skeletal muscle DicerSOMhet PKRnull MosIR 2306 biol rep 03

value: DicerSOM/wt Pkr-/- Tg(MosIR)


title: skeletal muscle DicerSOMhet PKRnull MosIR 2306 biol rep 02


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep3

value: Lung


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep1


title: Keratinocytes, siCtrl, input, rep1


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep2


title: skeletal muscle wt 2306 biol rep 03


title: skeletal muscle DicerDHEL1het PKRnull MosIR 2306 biol rep 02

value: Dicer-delta-HEL1/wt Pkr-/- Tg(MosIR)


title: Lung of rat exposed to 100% oxygen at 8000 ft for 5 h, biological rep4


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep4


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep3


title: Lung of rat exposed to 21% oxygen at 8000 ft for 5 h, biological rep4


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep4


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep1


title: cMPTP_ACSA2 cells_MPTP3 Mdb

city: Pamplona

first: Maria S.

last: Aymerich

state: Navarra

address: Calle Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: Universidad de Navarra

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 genome using Kallisto
Calculate raw counts with Kallisto
Assembly: mm10
Supplementary files format and content: abundance files from Kallisto

molecule: polyA RNA

source_name: Midbrain

extract_protocol:
Samples were prepared with the Illumina TruSeq Stranded mRNA kit following manufacturer’s indications and sequenced as reverse paired-end (50 bp) runs on the Nextseq sequencer
Truseq mRNA (Illumina)
full length strand specific mRNA sequencing

value: Midbrain

value: ACSA2+ cells


title: skeletal muscle DicerSOMhet PKRnull MosIR 2306 biol rep 01


title: skeletal muscle DicerDHEL1het PKRnull MosIR 2306 biol rep 03


title: skeletal muscle wt 2306 biol rep 01


title: skeletal muscle DicerDHEL1het PKRnull MosIR 2306 biol rep 01


title: Lung of rat exposed to 21% oxygen at 8000 ft for 10 h, biological rep1


title: cMPTP_ACSA2 cells_MPTP2 Mdb


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep4


title: cMPTP_ACSA2 cells_MPTP1 Mdb


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep1


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep2


title: Lung of rat exposed to 21% oxygen at 4000 ft for 5 h, biological rep3


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep3


title: Lung of rat exposed to 100% oxygen at 4000 ft for 5 h, biological rep2


title: single-Jk5-single-Igh_v-Abl_IGCR1CBE1_rep1

description: aligned to AJ851868/mm9 hybrid genome

data_processing:
Standard basecalling formats for Miseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp
Assembly: AJ851868/mm9 hybrid genome
Supplementary files format and content: Tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paired end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)
Library strategy: 3C-HTGTS

extract_protocol:
Cells were fixed with 2% formaldehyde, quenched with glycine, lysed in a lysis buffer containing: 150mM NaCl, 0.5% NP-40, 1% Triton X-100, 50mM Tris-HCl pH7.5, 5mM EDTA pH8.0. Nuclei were digested with NlaIII, ligated with T4 DNA Ligase, treated with Proteinase K and RNase A prior to DNA precipitation.
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primers

treatment_protocol:
Pre-B cells were isolated from mouse bone marrow by FACS sorting for B220+ CD43low IgM- cells
G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days

value: v-Abl transformed pro-B cell line

value: Rag2-/-, Emu-Bcl2, single Jk5-single Igh


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep2


title: Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep1


title: Igh-Igk-hybrid-Vk_v-Abl_IGCR1CBE1_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-Vk


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep4


title: cMPTP_ACSA2 cells_Ctrl2 Mdb


title: Igh-Igk-hybrid-Vk_v-Abl_IGCR1CBE1_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep3


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep2


title: Lung of rat exposed to 100% oxygen at 0 ft for 5 h, biological rep1


title: Igh-Igk-hybrid-Vk_v-Abl_IGCR1CBE1_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: single-Jk5-single-Igh_v-Abl_IGCR1CBE1_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: cMPTP_CD11b cells_MPTP3 Mdb

value: CD11b+ cells


title: TDN iPSC NK 2- ML

city: San Diego

first: Dan

middle: S

last: Kaufman

state: California

address: 2880 Torrey Pines Scenic Dr

department: School of Medicine

institute: University of California San Diego

data_processing:
nf-core RNAseq version 3.14
Sequences  were processed with all default settings of the nf-core pipeline
Counts were generated with the Psuedo alignment program salmon, version 1.10 using Human genome build GRCh38 and Ensembl gene annotation version 110
Assembly: GRCh38
Supplementary files format and content: tab delimited files containing the transcript counts for each sample (columns) and all transcripts (rows)
Supplementary files format and content: tab delimited files containing the transcript TPM values for each sample (columns) and all transcripts (rows)
Supplementary files format and content: tab delimited files containing the gene counts for each sample (columns) and all transcripts (rows)
Supplementary files format and content: tab delimited files containing the gene TPM values for each sample (columns) and all transcripts (rows)

source_name: WT iPSC derived

growth_protocol: To analyse the gene expression and transcriptome expression profiles of WT, TGFBR2-KO and TGFBR2-DN iPSC NK cells, we cultured them in either our standard NK cell culture conditions with IL-2 (100U/mL) and IL-15 (10ng/mL) or memory like (ML) NK cell culture condition using IL-12/15/18 stimulation followed by cultured in IL-2 and 15 for one week as described previously.

extract_protocol:
Total RNA were Isolated using Qiagen RNA isolation Kit using manufacturer protocol
The libraries were prepared for RNA samples using the Illumina Stranded mRNA Library Prep Kit, targeting mRNA via poly-A selection for strand-specific cDNA synthesis.
The libraries were prepared for RNA samples using the Illumina Stranded mRNA Library Prep Kit, targeting mRNA via poly-A selection for strand-specific cDNA synthesis. The libraries were sequenced using Illumina Novaseq X+ in the IGM Genomics Center at UCSD.

treatment_protocol: Standard NK cell culture conditions with IL-2 (100U/mL) and IL-15 (10ng/mL) or memory like (ML) NK cell culture condition using IL-12/15/18 stimulation followed by cultured in IL-2 and 15 for one week

value: WT iPSC derived

value: NK cells

value: WT

value: IL-12/IL-15/IL18 treated


title: cMPTP_ACSA2 cells_Ctrl1 Mdb


title: cMPTP_CD11b cells_MPTP2 Mdb


title: single-Jk5-single-Igh_v-Abl_CerCBE1_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: TKO iPSC NK 2 -ML

value: Standard culture condition


title: TKO iPSC NK 1-ML


title: WT iPSC NK 2-ML

source_name: TGFBR2-KO iPSC derived

value: TGFBR2-KO iPSC derived

value: TGF-beta Knockout

value: IL-12/IL-15/IL18  treated


title: TDN iPSC NK 1 -ML


title: cMPTP_CD11b cells_Ctrl3 Mdb


title: cMPTP_CD11b cells_MPTP1 Mdb


title: WT iPSC NK 1-ML


title: cMPTP_ACSA2 cells_Ctrl3 Mdb


title: BM-preB_CerCBE1_rep2

description: aligned to AJ851868/mm9 hybrid genome

source_name: bone marrow pre-B cells

value: bone marrow pre-B cells

value: Rag2-/-, VH7-3 Igh pre-rearranged

value: pre-B cell isolation from mouse bone marrow


title: TDN iPSC NK 2-Std


title: cMPTP_CD11b cells_Ctrl1 Mdb

value: Midbrain


title: TKO iPSC NK 1-Std

source_name: TGFBR2-DN iPSC derived

value: TGFBR2-DN iPSC derived

value: TGF-beta Knockdown


title: BM-preB_CerCBE1_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: WT iPSC NK 2 -Std


title: TKO iPSC NK 2-Std


title: v-Abl_CerCBE1_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line

value: Rag2-/-, Emu-Bcl2


title: cMPTP_CD11b cells_Ctrl2 Mdb

value: CD11b+ cells


title: WT iPSC NK 1 - Std


title: v-Abl_CerCBE1_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: cMPTP_ACSA2 cells_MPTP2 Str

source_name: Striatum

value: Striatum

value: ACSA2+ cells


title: single-Jk5-single-Igh_v-Abl_CerCBE1_rep1

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-single Igh


title: Control 7

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Medicine

description:
normalized_Gene TPM_PE_ctrl.csv
normalized_Gene read counts_PE_Ctrl.csv

data_processing:
FASTX-Toolkit and Trimmomatic were used to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases.
Salmon was used to build index and align the reads
Quantified data was checked for GC content and gene length biases using R package NOISeq
Mean variance and PCA were computed between biological replicates using the tximport package
The differential expression analysis was conducted using the DESeq2 package
Assembly: hg19
Supplementary files format and content: normalized_Gene TPM_PE_ctrl.csv
Supplementary files format and content: normalized_Gene read counts_PE_Ctrl.csv
Supplementary files format and content: normalized_TPM_EPS8L1_OE.xlsx

source_name: BEWO

growth_protocol: Wild-type SGHPl-4 cells were transfected with pT2B-puro Sleeping Beauty construct containing the EPS8L1 overexpression cassette. BeWo cells depleted PSG9 expression by RNAi strategy and simultaneously subjected the cells to forskolin treatment followed by transcription analysis.

extract_protocol:
Total RNA was extracted by using RNeasy Mini kit 250 (Qiagen) and atleast 1ug RNA was used to prepare library in SGHPL cells. From BeWo cells the RNA extraction was carried out with the Direct-zol™ RNA MiniPrep Kit (#R2025 Zymo Research). Then 500 ng ~ 1 µg total RNA was used to synthesize single-stranded cDNA with the High-Capacity RNA-to-cDNA™ Kit (#4387406 Thermo Fisher Scientific) following the manufacturer’s instructions.
The total RNA was extracted from the cells at 48 hr post-Forskolin treatment. The quality control (QC) of all RNA samples, including concentration, 28S/18S ration and RNA integrity number (RIN) were performed with the Agilent 2100 Bioanalyzer System. The transcriptome of 12 RNA samples were prepared with the stranded mRNA library kit and sequenced on the ‘DNBseq’ platform at BGI Group.

treatment_protocol: Puromycin selection (3 μg/ml) was carried out for 15 days for stable EPS8L1 overexpression with regular media including DMEM/ F12-GlutaMAX supplemented with 10.00% (v/v) FBS and 1.00% Antibiotic-Antimycotic (AA). Wild type cells were grown in regular media only without puromycin. BeWo cells were maintained in GlutaMAXTM DMEM/F-12 (#31331028 Thermo Fisher Scientific) medium supplemented with 10.00% (v/v) Foetal Bovine Serum (FBS) and 1.00% (v/v) penicillin/streptomycin (P/S). Saint Georges Hospital Placental cell Line-4 (SGHPL-4) were cultured in the Ham's F-10 liquid medium (#FG0715) supplemented with 10.00% FBS and 1.00% P/S. All cells were cultured in 5.00% CO2 at 37°C. The LipofectamineTM 3000 Reagent (#L3000015 Thermo Fisher Scientific) and the NeonTM Transfection System (#MPK5000 Thermo Fisher Scientific) were used for BeWo and SGHPL4 cells respectively following the manufacturer’s instructions. (Optional: To obtain the stable cell lines with the Sleeping Beauty (SB) system -78 transfected cells were further selected with the complete medium containing ~ 4 µg/ml Puromycin for 10 ~ 14 days.)

value: BEWO

value: Syncyiotrophoblast

tag: group

value: Control (patient healthy control from Placenta)

value: forskolin


title: Control 6


title: Control 3


title: Control 8


title: v-Abl_SisCBE2_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Control 5


title: Control 2


title: cMPTP_ACSA2 cells_MPTP3 Str


title: cMPTP_ACSA2 cells_MPTP1 Str


title: Preeclampsia sample 10

value: Patient diseased (depleted PSG9 expression by RNAi strategy)


title: Control 1


title: Control 4


title: v-Abl_SisCBE2_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: TDN iPSC NK 1-Std

value: TGFBR2-KO iPSC derived

value: NK cells

value: TGF-beta Knockout

value: Standard culture condition


title: cMPTP_ACSA2 cells_Ctrl3 Str


title: v-Abl_iEk_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: cMPTP_ACSA2 cells_Ctrl2 Str


title: cMPTP_ACSA2 cells_Ctrl1 Str


title: Preeclampsia sample 9


title: Preeclampsia sample 7


title: Preeclampsia sample 8


title: cMPTP_CD11b cells_MPTP3 Str


title: Preeclampsia sample 6


title: DJH-INV_v-Abl_untreated_JH4_rep2

description: aligned to mm9_DQ52JH4 genome

value: Rag1-/-, Emu-Bcl2, OsTIR1, WAPL-degron, single Igh, DJH-INV

value: RAG1&2 complementation, G1-arrest, untreated


title: single-Jk5-single-Igh_v-Abl_CerCBE1_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: v-Abl transformed pro-B cell line


title: v-Abl_iEk_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2


title: BAP-IL13-49

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

data_processing:
Reads were annotated and mapped to the human genome assembly GRCh38.p12 using HISAT
Differential expression (q<0.05) was determined in DESeq2  compared to vehicle control.
Assembly: GRCh38.p12
Supplementary files format and content: Processed data files are normalized read counts with corresponding Entrez Gene ID after DESeq2 analysis

source_name: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days

growth_protocol: Primary HBEC (Lonza) were expanded and transferred to transwell inserts for differentiation at the air-liquid interface in 24-well plates each containing 500 uL of assay medium utilizing the PnuemaCult™ ALI medium kit (STEMCELL Technologies, Vancouver, CA).   Cells were cultured at 37C, 5% CO2 with media changes every 48 to 72 hours.  On day 10, 10 ug/mL interleukin-13 was added to media for cells to induce an asthmatic phenotype.  IL-13 was included in every media change after day 10 for cells to induce an asthmatic phenotype.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using RNeasy Mini Kits (Qiagen) and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
mRNA was poly-A selected, and libraries were prepared as previously described (Dasgupta et al., 2022.

treatment_protocol: On day 25, inserts were washed with DPBS (pH 7.0 -- 7.3) and then exposed on the apical surface for 48 hours to either 25 uL 1% dimethyl sulfoxide (DMSO) with a DPBS vehicle or BAP (1 – 40 ug/mL) in DMSO with a DPBS vehicle.

value: 40 µg/ml benzo[a]pyrene (BAP)


title: Preeclampsia sample 5


title: cMPTP_CD11b cells_MPTP1 Str

value: Striatum

value: CD11b+ cells


title: BAP-IL13-48

value: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days


title: DJH-INV_v-Abl_untreated_JH4_rep1

description: aligned to mm9_DQ52JH4 genome


title: cMPTP_CD11b cells_MPTP2 Str


title: Preeclampsia sample 3

value: BEWO


title: cMPTP_CD11b cells_Ctrl2 Str


title: Igh-Igk-hybrid-D-JH_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, Igh-Igk hybrid-D-JH

value: RAG2 complementation, G1-arrest


title: Preeclampsia sample 4

value: Syncyiotrophoblast

value: forskolin


title: DJH-INV_v-Abl_untreated_JH4_rep3

description: aligned to mm9_DQ52JH4 genome


title: cMPTP_CD11b cells_Ctrl3 Str


title: Igh-Igk-hybrid-D-JH_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: Igh-Igk-hybrid-D-JH_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: Preeclampsia sample 2

value: Patient diseased (depleted PSG9 expression by RNAi strategy)


title: BAP-19

source_name: primary bronchial epithelial cells differentiated at air-liquid interface


title: BAP-IL13-46


title: Preeclampsia sample 1


title: cMPTP_CD11b cells_Ctrl1 Str


title: Igh-Igk-hybrid-D-JH_v-Abl_JH1-4_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: BAP-IL13-50


title: BAP-18

value: primary bronchial epithelial cells differentiated at air-liquid interface


title: Igh-Igk-hybrid-D-JH_v-Abl_JH1-4_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: sMPTP_ACSA2 cells_MPTP4 Mdb

value: Midbrain

value: ACSA2+ cells


title: Overexpressing-3 EPS8L1 SGHPl_4 cells P.15

description:
BGI-11
normalized_TPM_EPS8L1_OE.xlsx

source_name: SGHPL

value: SGHPL

value: OE

value: over expressed


title: sMPTP_ACSA2 cells_MPTP3 Mdb


title: BAP-17


title: Overexpressing-2 EPS8L1 SGHPl_4 cells P.17

description:
BGI-9
normalized_TPM_EPS8L1_OE.xlsx


title: IL13-35

value: vehicle control (PBS with 1% DMSO)


title: BAP-20

value: 40 µg/ml benzo[a]pyrene (BAP)


title: sMPTP_ACSA2 cells_MPTP2 Mdb


title: Overexpressing-1 EPS8L1 SGHPl_4 cells P.17

description:
BGI-6
normalized_TPM_EPS8L1_OE.xlsx


title: Igh-Igk-hybrid-D-JH_v-Abl_JH1-4_rep1

description: aligned to AJ851868/mm9 hybrid genome

source_name: v-Abl transformed pro-B cell line

value: v-Abl transformed pro-B cell line


title: sMPTP_ACSA2 cells_Ctrl3 Mdb


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep5

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-CerSis KO


title: Wild Type SGHPl_4 cells P.19

description:
BGI-4
normalized_TPM_EPS8L1_OE.xlsx

value: WT

value: untreated


title: sMPTP_CD11b cells_MPTP4 Mdb

value: CD11b+ cells


title: Wild Type SGHPl_4 cells P.16

description:
BGI-3
normalized_TPM_EPS8L1_OE.xlsx


title: sMPTP_ACSA2 cells_Ctrl2 Mdb


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep4

description: aligned to AJ851868/mm9 hybrid genome

value: RAG2 complementation, G1-arrest


title: Wild Type SGHPl_4 cells P.13

description:
BGI-1
normalized_TPM_EPS8L1_OE.xlsx

value: Syncyiotrophoblast


title: IL13-33

value: primary bronchial epithelial cells differentiated at air-liquid interface in the presence of 10 ug/mL IL-13 for 10 days


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: IL13-31


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome


title: sMPTP_CD11b cells_MPTP2 Mdb


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep1

description: aligned to AJ851868/mm9 hybrid genome


title: RPMI 8226 cells, RY (rep 3)

city: Geneva

first: Rafael

last: Rincon Perez

state: Geneva

address: Rue Michel Servet 1, 1221, Genève

country: Switzerland

institute: Université de Genève

data_processing:
After sequencing quality control (FastQC), the reads were aligned to the GRCh38 Ensembl human genome reference with STAR v.2.7.4.
The aligned reads were assessed for gene features with HTSeq v0.9.1 and the matrix of counts per genes was produced.
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR 1.34.1.
After normalization, the poorly detected genes were filtered out and out of 60,666 total genes, 21,394 genes with a count above 10 were kept.
Among them, only those genes with a fold change 2 threshold and a p-value < 0.05 (with a false discovery rate of 5%) were considered as differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including raw counts for all samples
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including normalized counts (cpm) for all samples
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including differentially expressed genes (DEG, FC > 2, FDR 5%) between HDAC6 KO and WT cell lines
Supplementary files format and content: Microsoft Excel worksheet (xlsx) including differentially expressed genes (DEG, FC > 2, FDR 5%) between HDAC6 RY and WT cell lines

source_name: RPMI 8226

growth_protocol: RPMI 8226 multiple myeloma cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Aurum™ total RNA mini kit (Bio-Rad)
Library TruSeq HT stranded

value: RPMI 8226

value: Multiple myeloma

value: HDAC6 RY


title: RPMI 8226 cells, RY (rep 2)


title: CON-2

value: primary bronchial epithelial cells differentiated at air-liquid interface


title: CON-3


title: IL13-34


title: sMPTP_CD11b cells_Ctrl3 Mdb

value: Midbrain


title: RPMI 8226 cells, RY (rep 1)


title: RPMI 8226 cells, KO (rep 2)

value: HDAC6 KO


title: sMPTP_CD11b cells_Ctrl2 Mdb


title: single-Jk5-Sis-KO_v-Abl_Jk5_rep2

description: aligned to AJ851868/mm9 hybrid genome

value: Rag2-/-, Emu-Bcl2, single Jk5-Sis KO


title: single-Jk5-CerSis-KO_v-Abl_Jk5_rep6

description: aligned to AJ851868/mm9 hybrid genome


title: CON-1

value: vehicle control (PBS with 1% DMSO)


title: single-Jk5-Sis-KO_v-Abl_Jk5_rep3

description: aligned to AJ851868/mm9 hybrid genome


title: sMPTP_ACSA2 cells_Ctrl1 Mdb

value: ACSA2+ cells