title: Mac1cell_R67_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C60

status: Public on Oct 01 2019

type: SRA

city: Houston

first: Qingnan

last: Liang

state: TX

address: One Baylor Plaza

department: HGSC

country: USA

institute: Baylor College of Medicine

description: P1_Mac.txt (matrix)

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: retina

extract_protocol:
Single nuclear capture and sequencing were performed on the ICELL8 single cell platform (Wafergen Biosytems). ICELL8 platform comprised of a multi-sample nano-dispenser that precisely dispensed 50nl of the single nuclei suspension into an ICELL8 nanowell microchip-containing 5184 wells (150nl capacity). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy of the microchip was performed using an Olympus BX43 fluorescent microscope with a robotic stage to visualize wells containing single nuclei (see Table 1 for single cell capture number across different experimental repeats). The automated well selection was performed using the CellSelect software (Wafergen Biosystems), which identified nanowells containing single nuclei and excluded wells with >1 nuclear, debris, nuclei clumps or empty wells. The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multi-sample nano-dispenser to candidate wells. Each well had a preprinted primer that contains an 11-nucleotide-well-specific barcode. This barcode was added to the 3’ (A)n RNA tail of the nuclear transcripts during reverse transcription and cDNA amplification, the latter of which was performed on candidate wells using SCRB-seq chemistry. After RT, the cDNA products from candidate wells were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified using 0.6x AMPure XP beads. A 3’ transcriptome enriched library was made using Nextera XT Kit and 3’-specific P5 primer, which was sequenced on the Illumina Hiseq2500.

treatment_protocol: Nuclei from frozen neural retinal tissue was isolated using RNase-free lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl¬2, 0.1% NP40). The frozen tissue was resuspended in ice-cold lysis buffer and triturated to break the tissue structure. The tissue aggregates were then homogenized using a Wheaton™ Dounce Tissue Grinder and centrifuged (500g) to pellet the nuclei. The pellet was re-suspended in fresh lysis buffer and homogenized to yield clean single-nuclei suspension. The collected nuclei were stained with DAPI (4',6-diamidino-2-phenylindole, 10ug/ml) and were diluted to 1000 μl of 3E4/ml with 1× PBS (without Ca and Mg ions, pH 7.4, Thermo Fisher), RNase inhibitor (NEB, 40KU/ml) and Cell Diluent Buffer.

tag: sample

tag: tissue

value: Retina


title: Mac1cell_R66_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R67_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R67_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R67_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R66_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R65_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R64_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R63_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R62_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R61_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R60_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R5_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R59_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R58_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R57_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R56_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R55_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R54_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R53_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R52_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R51_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R4_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R49_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R48_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R47_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R46_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R45_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R44_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R43_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R50_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R41_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R42_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R40_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C26

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R3_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R38_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R39_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R37_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R36_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R35_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R34_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C14

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R33_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R32_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R31_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R30_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R2_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C62

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R28_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R29_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C8

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C4

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R26_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R27_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C60

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R25_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C33

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R24_C13

description: P1_Mac.txt (matrix)


title: Z1163

city: Dallas

first: Sara

middle: K

last: Hildebrand

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

description:
HET_HSPC_cells_2
HSPCs_gene_exp.diff

data_processing:
fastq files were aligned to version mm10 of mouse reference genome using tophat v2.0.10
BAM files resulting from the alignments were run through cuffdiff v2.1.1 for differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: HSPCs

growth_protocol: Wild-type and Snrnp40-KO EL4 cells were routinely maintained in DMEM medium with 10% horse serum (cultures typically between 1 x 10e5 and 1 x 10e6 cells/mL).

extract_protocol:
Total RNAs from the cells were extracted using the RNeasy Plus kit with genomic DNA elimination (Qiagen), according to the manufacturer’s instructions.
Libraries were prepared using the KAPA Stranded RNA-Seq kit with RiboErase (HMR) (Kapa Biosystems), according to the manufacturer’s instructions.

treatment_protocol: EL4 cells were untreated or treated with PMA/ionomycin (50 ng/ml PMA and 1 ug/ml ionomycin) for 4 h. No treatment for primary HSPCs and T cells.

tag: background strain

tag: genotype

value: swp/+

tag: treatment

value: untreated


title: Mac1cell_R23_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C67

description: P1_Mac.txt (matrix)


title: Z1160

description:
WT_HSPC_cells_2
HSPCs_gene_exp.diff

value: wild-type


title: Z1159

description:
WT_HSPC_cells_1
HSPCs_gene_exp.diff


title: Z1167

description:
CMPDHET_HSPC_cells_3
HSPCs_gene_exp.diff

value: swp/rplc


title: Mac1cell_R23_C9

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C56

description: P1_Mac.txt (matrix)


title: Z1162

description:
HET_HSPC_cells_1
HSPCs_gene_exp.diff


title: Z1165

description:
CMPDHET_HSPC_cells_1
HSPCs_gene_exp.diff


title: Mac1cell_R23_C16

description: P1_Mac.txt (matrix)


title: Z1161

description:
WT_HSPC_cells_3
HSPCs_gene_exp.diff


title: Mac1cell_R23_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C7

description: P1_Mac.txt (matrix)


title: Z1164

description:
HET_HSPC_cells_3
HSPCs_gene_exp.diff


title: Mac1cell_R23_C15

description: P1_Mac.txt (matrix)


title: Mac1cell_R23_C3

description: P1_Mac.txt (matrix)


title: Z1158

description:
CMPDHET_T_cells_3
T_cells_gene_exp.diff

source_name: T-cells


title: Z1166

description:
CMPDHET_HSPC_cells_2
HSPCs_gene_exp.diff


title: Mac1cell_R25_C67

description: P1_Mac.txt (matrix)


title: Z1157

description:
CMPDHET_T_cells_2
T_cells_gene_exp.diff


title: Z1155

description:
HET_T_cells_3
T_cells_gene_exp.diff


title: Z1156

description:
CMPDHET_T_cells_1
T_cells_gene_exp.diff


title: Z1151

description:
WT_T_cells_2
T_cells_gene_exp.diff


title: Z1154

description:
HET_T_cells_2
T_cells_gene_exp.diff


title: Mac1cell_R22_C6

description: P1_Mac.txt (matrix)


title: Z1153

description:
HET_T_cells_1
T_cells_gene_exp.diff


title: Mac1cell_R22_C60

description: P1_Mac.txt (matrix)


title: Z1152

description:
WT_T_cells_3
T_cells_gene_exp.diff


title: Mac1cell_R22_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C70

description: P1_Mac.txt (matrix)


title: 6055G: matKO_2

city: Pittsburgh

first: Erik

last: Koppes

state: PA

address: 204 Craft Ave

department: MWRI

institute: University of Pittsburgh

data_processing:
Adapter Trim and QC: trim_galore --paired --retain_unpaired --output ./$OUTPUT
Alignment Mapping: STAR v2.7.0e; outFilterIntronMotifs RemoveNoncanonicalUnannotated; --chimOutType Junctions;  --twopassMode Basic; --outSAMtype BAM SortedByCoordinate
Feature Counts: HTSeq0.11.2 htseq-count --format bam --order pos --mode intersection-strict --nonunique none --minaqual 1 --stranded reverse --type exon --idattr gene_id --additional-attr gene_name
Diffential Expression: DESeq2
Genome_build: MmusGRC38.96 (ensembl)
Supplementary_files_format_and_content: csv (output from DEseq2)

source_name: Placenta

extract_protocol:
RNeasy Column(6188C,D; 6232B,D) or Trizol (6055E,F,G,H)
Illumina Paired-end TruSeq; poly-A capture; FR-first-strand

value: Placenta

tag: gestational age (dpc)

tag: Sex

value: Male

tag: sample id (litter and placenta)


title: 6232B: matKO_3


title: 6232D: matKO_4


title: Mac1cell_R22_C5

description: P1_Mac.txt (matrix)


title: 6055F: matKO_1


title: Z1150

description:
WT_T_cells_1
T_cells_gene_exp.diff


title: 6188D: WT_4

value: WT


title: Mac1cell_R22_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C55

description: P1_Mac.txt (matrix)


title: 6188C: WT_3


title: Mac1cell_R22_C44

description: P1_Mac.txt (matrix)


title: 6055H: WT_2


title: Mac1cell_R22_C3

description: P1_Mac.txt (matrix)


title: 6055E: WT_1


title: Mac1cell_R22_C39

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C67

description: P1_Mac.txt (matrix)


title: Tg-5 EE

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming, UMI extraction and sequence trimming in FASTQ files, fastp version 0.20.0 was used.
Cleaned read sequences were aligned with STAR version 2.7.0f
Molecule counting for exonic regions was performed with subread featureCounts version 1.6.0 and UMI-tools.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated text file with gene identifier (Ensembl) and UMI count columns.

molecule: polyA RNA

source_name: colon

extract_protocol:
The upper colon tissues section (2-3 cm piece) was taken from the WT and TG mice (SE and EE conditions). Colon was then prepared rapidly on ice, feces material was flushed with PBS and then colon tissue was rinsed again with PBS and rinsed tissue was briefly dried on tissue towel to remove excess PBS. The rinsed colon tissue was then collected in cryotubes and snap frozen by liquid N2 and stored  at -80 0C until use.
Sequencing libraries have been prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina following the manufacturer's handbook.

value: colon

tag: condition

value: enhanced environment

tag: genotype/variation

value: transgenic mouse model overexpressing the complete human SNCA genes modeling familial and sporadic forms of Parkinson's disease


title: Mac1cell_R22_C31

description: P1_Mac.txt (matrix)


title: Tg-4 EE


title: Mac1cell_R22_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R22_C24

description: P1_Mac.txt (matrix)


title: Tg-3 EE


title: Tg-1 EE


title: Mac1cell_R22_C12

description: P1_Mac.txt (matrix)


title: WT-5 EE

value: wild type


title: Mac1cell_R22_C52

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C65

description: P1_Mac.txt (matrix)


title: WT-3 EE


title: Mac1cell_R21_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C64

description: P1_Mac.txt (matrix)


title: WT-2 EE


title: Mac1cell_R21_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C63

description: P1_Mac.txt (matrix)


title: WT-1 EE


title: Tg-5 SE

value: standard environment


title: Tg-4 SE


title: Mac1cell_R21_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C59

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C58

description: P1_Mac.txt (matrix)


title: Tg-2 SE


title: Tg-2 EE


title: Tg-1 SE


title: Mac1cell_R21_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C48

description: P1_Mac.txt (matrix)


title: WT-3 SE


title: WT-4 EE


title: Mac1cell_R21_C47

description: P1_Mac.txt (matrix)


title: WT-2 SE


title: Mac1cell_R21_C3

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C36

description: P1_Mac.txt (matrix)


title: WT-5 SE


title: Mac1cell_R21_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C32

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C25

description: P1_Mac.txt (matrix)


title: YAP1_1_NIH3T3_CUT&RUN

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Following sequencing of CUT&RUN libraries, raw paired-end reads were aligned to the mm9 genome according to (Skene et al., 2018). Briefly, fastq files were mapped using Bowtie2 (version v2.2.5) with the following options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. For mapping Yeast spike-in fragments, we used the following options in addition to those stated directly above: --no-overlap --no-dovetail. Peak calling was performed as described in (Liu et al., 2018). In short, peaks were called from aligned BAM files using MACS2 callpeaks with the narrowPeak option and a P-value cutoff of 1e-5. Footprint detection was carried out by aligning all mapped read ends around motif containing peak centers. Peaks were centered around motifs using HOMER. Fragment ends were piled up using scripts previously published and available at: https://github.com/peteskene. For the final Yap CUT&RUN peak calling, mm9 aligned BAM files derived from both YAP5SA-NIH3T3 cells and control NIH3T3 cells were combined. Processed data from replicates was merged and converted to bigWig format for visualization.

molecule: genomic DNA

source_name: NIH3T3 cells grown in vitro

growth_protocol: NIH3T3 cells were grown under standard cell culture conditions in DMEM media supplemented with 10% FBS.

extract_protocol: Briefly, approximately 200,000 NIH3T3 cells were washed in wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine and complete protease inhibitor (EDTA-free, Roche), captured with Concanavalin A beads (Polysciences, Warrington, PA) and incubated with primary antibodies overnight at 4°C. After washing with Dig-wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.08% Digitonin and protease inhibitors), cells were resuspended in 50 μL Digwash buffer and 2.5 μL of protein A-MNase (1:10 diluted, batch 6 from Steve Henikoff) and incubated at room temperature for 10 minutes. Cell pellets were washed again and placed in a 0°C metal block, and 2 mM of CaCl2 was added and incubated for 45 minutes. MNase reaction was terminated by the addition of 2XSTOP buffer and incubated at 37°C 10 minutes. Samples were then digested by proteinase K at 70°C for 10 minutes and DNA was extracted by ethanol precipitation. Library were prepared using KAPA Hyper Prep Kit (KAPA) and custom Y-shaped TruSeq adapters according to the manufacturer's instructions. The antibodies used were anti-Yap (Novus, NB110-58358), anti-H3K27ac (Abcam, ab4729), anti-H3K27me3 (Cell Signaling, 9733S), anti H3K4me3 (Diagenode, C15410003), anti-CTCF (Diagenode, C15410210), anti-GABPA (ProteinTech, 215420-1), Gabpb1 (ProteinTech, 12597-1).

tag: cell line

tag: operation

tag: ip antibody

value: anti-Yap (Novus, NB110-58358)


title: H3K4me3_1_NIH3T3_CUT&RUN

value: anti H3K4me3 (Diagenode, C15410003)


title: YAP1_2_NIH3T3_CUT&RUN


title: H3K27ac_HiChIP_NIH3T3_2

data_processing:
Library strategy: HiChIP
H3K27ac HiChIP paired-end reads were aligned to the mm9 genome using HiC-Pro (Servant et al., 2015). Aligned reads were passed to the hichipper computational analysis pipeline (Lareau and Aryee, 2018), and loop calling was carried out with default parameters. For peak calling, we used “COMBINED, ALL”, and the MboI restriction fragment bed file for the mm9 genome was generated with the HiC-Pro digest_genome.py utility (digest_genome.py -r mboi). DNA loops that passed hichipper quality control were filtered to intrachromosomal loops with a minimum length of 5 Kbp and a maximum length of 2 Mbp. Tracks containing H3K27ac loop interactions calculated using the hichipper (--make-ucsc flag) were visualized using the WashU Epigenome browser and filtered according to interaction score. Virtual 4C (v4C) profiles were generated by visualizing dumped hic file outputs from Juicer (Durand et al., 2016a, 2016b) with a custom R script according to (Mumbach et al., 2017). The interaction output fro HiChIPPER was used for data visualization, and is provided as processed data.

extract_protocol: H3K27ac HiChIP was performed according to (Mumbach et al., 2017) with only minor modifications. Approximately 15 million NIH3T3 cells were used as input, and MboI digestion was carried out for 2 hours. We used anti-H3K27ac (Abcam, ab4729) . Cells were sonicated for 10 cycles (30 seconds on, and 30 seconds off) using a Bioruptor Pico instrument (Diagenode). For biotin pull down 150ng of chromatin was used as input, and tagementation was performed using 4 uL of Tn5 transposase. For post-PCR size selection we performed a double-sided size selection with Ampure XP beads (Beckmann-Coulter). All libraries were sequenced on a NextSeq 500 platform.

value: anti-H3K27ac (Abcam, ab4729)


title: H3K27ac_HiChIP_NIH3T3_1


title: H3K27me3_2_NIH3T3_CUT&RUN

value: anti-H3K27me3 (Cell Signaling, 9733S)


title: Mac1cell_R21_C27

description: P1_Mac.txt (matrix)

value: Retina


title: H3K27ac_2_NIH3T3_CUT&RUN


title: Tg-3 SE


title: Mac1cell_R21_C17

description: P1_Mac.txt (matrix)


title: WT-1 SE


title: H3K27ac_1_NIH3T3_CUT&RUN


title: Mac1cell_R21_C52

description: P1_Mac.txt (matrix)


title: H3K27me3_1_NIH3T3_CUT&RUN


title: Mac1cell_R21_C21

description: P1_Mac.txt (matrix)


title: GabpB1_2_NIH3T3_CUT&RUN

value: Gabpb1 (ProteinTech, 12597-1)


title: Mac1cell_R21_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C70

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R21_C14

description: P1_Mac.txt (matrix)


title: GabpB1_1_NIH3T3_CUT&RUN


title: GabpA_2_NIH3T3_CUT&RUN

value: anti-GABPA (ProteinTech, 215420-1)


title: CTCF_2_NIH3T3_CUT&RUN

value: anti-CTCF (Diagenode, C15410210)


title: Mac1cell_R20_C66

description: P1_Mac.txt (matrix)


title: CTCF_1_NIH3T3_CUT&RUN


title: Mac1cell_R20_C64

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C63

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C4

description: P1_Mac.txt (matrix)


title: Ctrl_MI_Dropseq

description:
MI_CF_DropSeq.scale.data.csv.gz
MI_CF_DropSeq.meta.data.csv
MI_CF_DropSeq.raw.data.csv.gz

data_processing: For DROP-seq, cells were co-encapsulated into nano-liter sized droplets containing barcoded microparticles (ChemGenes, catalog number Macosko201110) and lysis buffer using a custom microfluidics device (FlowJEM, Toronto, Canada). After droplet breakage, reverse transcription (Thermo), and exonuclease treatment (NEB) all cDNA was PCR amplified (KAPA), pooled, purified with Ampure XP beads (Beckman Coulter), and ran on a Fragment analyzer (Advanced Analytical Technologies, Inc.) for quality control, quantification, and size determination. Library preparation was performed with the Illumina Nextera XT kit, and libraries were triple purified with Ampure XP beads (Beckman Coulter). After sequencing, raw FastQ files were converted to BAMs with Picard tools (MergeSamFiles) and then used is input for STAR alignment, cell barcode correction, and digital gene expression (DGE) matrix generation via the Droplet-based RNA-seq tools software package (available at http://mccarrolllab.com/dropseq/). We provided the metadata, raw data, and scaled data output from Seurat as out processed data files.

source_name: Heart tissue

extract_protocol: Whole heart tissue was dissociated via Langendorff repurfusion. Next, single cells were washed prior to loading into a custom Drop-seq rig.

value: Tcf21-iCRE; mTmG

value: Heart

value: Myocardial Infarction


title: Ctrl_Sham_Dropseq_2

description:
Sham_CF_DropSeq.scale.data.csv.gz
Sham_CF_DropSeq.meta.data.csv
Sham_CF_DropSeq.raw.data.csv.gz

value: Sham


title: NIH3T3_ATAC_2

description: NIH3T3_ATAC_merged.tagdir.ucsc.bedGraph.bigWig

data_processing: ATAC-seq reads were mapped to the mouse genome (mm9) using Bowtie2 with default paired-end settings. Next, all non-nuclear and unmapped paired reads were discarded. Duplicated reads were removed with the picard MarkDuplicates function, default settings. Processed data from replicates was merged and converted to bigWig format for visualization.

extract_protocol: Cardiac fibroblasts, Tcf21 lineage GFP positive,  were isolated from hearts  by langendorff perfusion. Sorted cells were spun down and lysed prior to tagmentation according to the Fast-ATAC-seq protocol (Corces et al., 2016). Briefly For Fast-ATAC (ATAC-seq), sorted cells were spun down, FACS buffer was removed, the pellet was then re-suspended in a transposase-containing reaction mixture complete with 0.05% digitonin prior to tagmentation at 370C with 1000 rpm agitation for 30 minutes. Next, transposed DNA was purified with a Qiagen PCR MinElute kit (Qiagen 28004). Fast-ATAC libraries were purified with a 1.8X SPR purification using AMPure XP beads following PCR amplification.


title: Mac1cell_R20_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C50

description: P1_Mac.txt (matrix)


title: LatsCKO_ATAC_MI_2

source_name: Cardiac fibroblasts FACS sorted for GFP, Tcf21 lineage marker

value: Tcf21-iCre; Lats1flox/flox; Lats2flox/flox ; mTmG

tag: cell type


title: Ctrl_Sham_Dropseq_1


title: Mac1cell_R20_C53

description: P1_Mac.txt (matrix)


title: LatsCKO_ATAC_MI_1

value: Cardiac fibroblasts FACS sorted for GFP, Tcf21 lineage marker


title: Mac1cell_R20_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C49

description: P1_Mac.txt (matrix)


title: GabpA_1_NIH3T3_CUT&RUN


title: Mac1cell_R20_C48

description: P1_Mac.txt (matrix)


title: LatsCKO_ATAC_Sham_2


title: LatsCKO_ATAC_Sham_1


title: Mac1cell_R20_C42

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C35

description: P1_Mac.txt (matrix)


title: Ctrl_ATAC_MI_2


title: Mac1cell_R20_C30

description: P1_Mac.txt (matrix)


title: Ctrl_ATAC_Sham_1


title: Ctrl_ATAC_MI_1


title: NIH3T3_ATAC_1


title: Mac1cell_R20_C13

description: P1_Mac.txt (matrix)


title: LatsCKO_MI_Dropseq


title: Mac1cell_R20_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R20_C21

description: P1_Mac.txt (matrix)


title: Ctrl_ATAC_Sham_2


title: LatsCKO_Sham_Dropseq


title: Mac1cell_R1_C6

description: P1_Mac.txt (matrix)


title: BMDCs, Arhgef2-KO AP3 rep2

first: Hans-Christian

last: Reinecker

state: Texas

address: J5.136, 5959 Harry Hines Boulevard

department: Medicine

institute: University of Texas Southwestern Medical Center

data_processing:
Blc2fastq2 Conversion software (Illumina) was used to generate de-multiplexed Fastq files.
Illumina reads were post-processed and aligned to the mouse mm10 assembly using Tophatprogram with default parameters in the DNAnexus.
Expression values were normalized as Fragments per Kilobase Million reads after correction for gene length (FPKM) in Cuffdiff version 1.05 in the DNAnexus
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: Bone Marrow-derived Dendritic cells (BMDCs)

growth_protocol: Bone marrow-derived dendritic cells (BMDCs) cells were generated by flushing bone marrow cells from femurs and tibia of WT or indicated knockout (KO) mice, depleting red blood cells using ACK lysis buffer, and resuspending cell in complete RPMI-1640 media supplemented with 10% FBS, 0.5% penicillin/streptomycin mixture, 10 ng/ml GM-CSF and 10 ng/ml IL-4. Cells were maintained in culture at 37 °C, 5%CO2 for 6 days before experimentation.

extract_protocol:
500ng of total RNA was subjected to library synthesis using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adaptors according to the manufacturer’s protocol (Illumina).
Total RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2. BMDCs were stimulated in FCS 10% RPMI-1640 with or without ansamitocin-P3 (100nM) for 5 hours.

tag: strain

value: C57BL/6 background

value: 100nM of ansamitocin-P3 (AP3)

tag: time


title: BMDCs, Arhgef2-KO AP3 rep1

value: Bone Marrow-derived Dendritic cells (BMDCs)


title: BMDCs, Arhgef2-KO NT rep2

value: NT (No treatment)


title: Mac1cell_R1_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C57

description: P1_Mac.txt (matrix)


title: BMDCs, Arhgef2-KO NT rep1


title: BMDCs, WT AP3 rep1

value: WT


title: nmf219/nmf219_5

city: Bar Harbor

first: Ken

last: Johnson

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
CPM
Genome_build: ensembl genes
Supplementary_files_format_and_content: CPM

source_name: inner ear

extract_protocol:
inner ear were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: inner ear

tag: age


title: Mac1cell_R1_C54

description: P1_Mac.txt (matrix)

tag: sample


title: BMDCs, WT NT rep2


title: Mac1cell_R1_C52

description: P1_Mac.txt (matrix)

tag: tissue


title: Mac1cell_R1_C51

description: P1_Mac.txt (matrix)


title: WT_5


title: Mac1cell_R1_C4

description: P1_Mac.txt (matrix)


title: WT_4


title: Mac1cell_R1_C37

description: P1_Mac.txt (matrix)


title: nmf219/nmf219_3


title: Mac1cell_R1_C40

description: P1_Mac.txt (matrix)


title: nmf219/nmf219_4


title: BMDCs, WT AP3 rep2


title: WT_3


title: Mac1cell_R1_C35

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C36

description: P1_Mac.txt (matrix)


title: WT_2


title: Mac1cell_R20_C0

description: P1_Mac.txt (matrix)


title: BMDCs, WT NT rep1


title: Mac1cell_R1_C26

description: P1_Mac.txt (matrix)


title: nmf219/nmf219_2


title: Mac1cell_R1_C20

description: P1_Mac.txt (matrix)


title: Phf21b_ATAC_N2A_siPhf21b_D2_df_Replicate1

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

description: ATAC-seq in N2A

data_processing:
For the ATAC-Seq samples, sequenced reads were aligned to mouse reference genome (mm9) using Bowtie v0.12.9 with the following parameters; [bowtie -S -p 10 -X 2000]. SAMTOOLS v0.1.19 was used to convert the SAM file into BAM format and to sort and index the BAM file. From the sorted BAM file, peak calling was performed using MACS2 v2.0.10 with  BAMPE option. Generation of WIG files, and calculation of enrichment scores above input for each of the peaks were performed using QuasR.
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

growth_protocol:
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.  For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.

extract_protocol:
For ATAC seq the protocol from Buenrostro was followed.
Libraries for ATAC seq were prepared using Nextera DNA Sample Preparation Kit.

treatment_protocol: (1) For ES cell ChIP and RNA seq: Transgenic A2lox ES cells harboring the murine Phf21b fused to an N-terminal HA-tag under the control of a doxycycline-inducible promoter were generated according to Iacovino et al (2011). Ectopic induction of Phf21b was achieved with 500 ng/ml doxycycline for 24 hours.2) ChIP-seq, ATAC seq and RNA seq  from  N2a day2  neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA. (3) For all siRNA-mediated knockdown experiments, cells were seeded and pre-depleted for two days by transfecting with ON-TARGETplus SMARTpool siRNAs (i.e., a mixture of 4 siRNAs provided as a single reagent from Dharmacon) every second day. For siRNA transfections, Lipofectamine RNAiMax was used according to the manufacturer's instructions. For N2a differentiation pre-depleted cells were differentiated by adding retinoic acid along with siRNAs for two days in N2a differentiation media.

tag: replicate

tag: developmental stage

value: Day2 differentiated


title: Mac1cell_R1_C32

description: P1_Mac.txt (matrix)

value: Retina


title: Mac1cell_R1_C11

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C46

description: P1_Mac.txt (matrix)


title: Mac1cell_R1_C19

description: P1_Mac.txt (matrix)


title: WT_1

tag: genotype


title: nmf219/nmf219_1


title: Phf21b_ATAC_N2A_siPhf21b_Undf_Replicate1

description: ATAC-seq in N2A

value: Undifferentiated


title: Mac1cell_R19_C69

description: P1_Mac.txt (matrix)


title: Phf21b_ATAC_N2A_siNTC_D2_df_Replicate2

description: ATAC-seq in N2A


title: Mac1cell_R19_C9

description: P1_Mac.txt (matrix)


title: Phf21b_ATAC_N2A_siNTC_D2_df_Replicate1

description: ATAC-seq in N2A


title: Mac1cell_R19_C68

description: P1_Mac.txt (matrix)


title: Phf21b_ATAC_N2A_siPhf21b_Undf_Replicate2

description: ATAC-seq in N2A


title: Phf21b_ATAC_N2A_siNTC_Undf_Replicate1

description: ATAC-seq in N2A


title: Mac1cell_R19_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C67

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C64

description: P1_Mac.txt (matrix)


title: Phf21b_ATAC_N2A_siNTC_Undf_Replicate2

description: ATAC-seq in N2A


title: Phf21b_ATAC_N2A_siPhf21b_D2_df_Replicate2

description: ATAC-seq in N2A


title: Mac1cell_R19_C54

description: P1_Mac.txt (matrix)


title: Phf21b_ChIP_N2A_Day2_Diff_Replicate1

description: ChIP-seq in N2A

data_processing:
For the ChIP-Seq samples, sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.9 and each read was aligned to maximally one position in the genome. SAMTOOLS v0.1.19 was used to convert the SAM file into BAM format and to sort and index the BAM file. Sorted BAM files were used for peak calling using MACS2 v2.0.10 with default parameters. For the UCSC genome browser track visualization, WIG files were obtained using the QuasR package .
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

extract_protocol:
For ChIP seq lysates were clarified from sonicated nuclei. For inducible ES ChIP, abcam HA antibody was used while for ChIP from N2a cells origene Phf21b endogenous antibody was used.
The library for ChIPseq samples were prepared using standard illumina library preparation kit.


title: Mac1cell_R1_C12

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C51

description: P1_Mac.txt (matrix)


title: Phf21b_RNA_IUE_shNTC_Replicate3

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shNTC_Replicate3

data_processing:
For the low-input in vivo RNA-Seq samples, sequenced reads were aligned to the mouse reference genome (mm9) with UCSC’s annotations using TopHat v2.0.8. Unique molecular identifiers (UMI) were added to the sorted bam file using AddUMIsToBam function in bamtools and then unique read count was calculated using picard-2.9.0 MarkDuplicates function with following option: [REMOVE_DUPLICATES=true BARCODE_TAG=RX ASSUME_SORTED=true]. SAMTOOLS v0.1.19 was used to convert the BAM output to SAM format and to sort the BAM file. From the aligned BAM files, the read counts per gene were calculated using the HTSeq program v0.5.4p1. Read counts from HTSeq program was normalized using DESeq program.
Genome_build: mm9
Supplementary_files_format_and_content: For the RNA-Seq samples, tab-delimited text files include DESeq normalized read counts for each Sample. For the ChIP-Seq and ATAC-Seq samples, wig files for UCSC genome browser track were provided.

growth_protocol:
For in vivo RNA seq, we carried out IUEs of progenitor cells at E13.5 mouse cortex and FACS sorted the electroporated cells 4 days after IUE.
Murine Neuro2a cells (N2a cells)  were cultured at 37°C in 7% CO2 and 88% relative humidity in 10 ml of DMEM supplemented with 10% fetal calf serum, 1× NEAA and 2 mM L-glutamine. Neuronal differentiation in N2A cells was induced by adding 20 μM retinoic acid in DMEM supplemented with 2% FBS, 1% Glutamine and 1% NEAA.  For ES cell experiments, ES159 cells on feeders were splitted every 2 days onto tissue culture dishes coated with 0.2% gelatin, and the media was changed daily. All ES cell experiments were performed at feeder-free five stage. In vitro neuronal differentiation was performed as described by Bibel et al (2004, 2007) where ES cells were directly plated on PORN/Laminin-coated tissue culture dishes and cultivated for 2 days in N2 media followed by complete media for induced neuron (iTN) formation.

extract_protocol:
RNA samples for in vivo RNA seq from cortex was FACS sorted  and isolated by RNeasy Micro Kit
RNA libraries for the in-vivo cortex RNA seq Ovation® SoLo RNA-Seq System was used.

value: E17.5 embryo

value: cortex

value: Wild type


title: Phf21b_RNA_IUE_shNTC_Replicate1

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shNTC_Replicate1


title: Mac1cell_R19_C57

description: P1_Mac.txt (matrix)


title: Phf21b_RNA_IUE_shNTC_Replicate2

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shNTC_Replicate2


title: Mac1cell_R19_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C48

description: P1_Mac.txt (matrix)


title: JUN-HA, replicate 2  [jun-2-irf4-GGCTAC_S10]

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

data_processing:
ChIP-seq reads were trimmed of adaptors with cutadapt
RPM bigwig: Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
RPM bigwig: Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
RPM bigwig: Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
RRPM bigwig: First aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference and unaligned reads then aligned to dm6 genome with same parameters
RRPM bigwig: Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates from both hg19 and dm6 mapped reads
RRPM bigwig: Normalization to 1M dm6 reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls.
Genome_build: RPM bigwig: hg19, RRPM bigwig:  hg19, dm6
Supplementary_files_format_and_content: RPM and RRPM bigwig; details in readme.txt

source_name: patient-derived CAR-T_JUN-HA

extract_protocol:
Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using Ampure XP
End-repair and A-tailing performed with NEB Ultra II Kit per protocol. Adaptor ligation and indexing with NEBNext Multiplex Oligos

value: patient-derived CAR-T

value: Retroviral transduction with JUN-HA construct

tag: growth protocol

value: T cell media + IL-2

tag: chip antibody


title: Phf21b_RNA_IUE_shPhf21b_Replicate1

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shPhf21b_Replicate1


title: JUN-HA, replicate 2  [jun-2-jun-CTTGTA_S11]

value: JUN (Active Motif, #39309)


title: Phf21b_RNA_IUE_shPhf21b_Replicate3

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shPhf21b_Replicate3


title: JUN-HA, replicate 1  [jun-1-jun-CAGATC_S6]


title: Mac1cell_R19_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C29

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C21

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C61

description: P1_Mac.txt (matrix)


title: HA only, replicate 2  [ha-2-irf4-GATCAG_S8]

source_name: patient-derived CAR-T_HA only

value: Retroviral transduction with HA construct


title: JUN-HA, replicate 1  [jun-1-irf4-GCCAAT_S5]


title: Mac1cell_R19_C16

description: P1_Mac.txt (matrix)


title: HA only, replicate 2  [ha-2-inp-ACTTGA_S7]


title: Mac1cell_R19_C11

description: P1_Mac.txt (matrix)


title: Phf21b_RNA_IUE_shPhf21b_Replicate2

description:
RNA-seq in vivo cortex
Normalized_counts_IUE.txt
IUE_shPhf21b_Replicate2


title: Mac1cell_R19_C45

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C10

description: P1_Mac.txt (matrix)


title: JUN-HA, replicate 2  [jun-2-inp-TAGCTT_S9]


title: Mac1cell_R18_C66

description: P1_Mac.txt (matrix)


title: Mac1cell_R19_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R18_C64

description: P1_Mac.txt (matrix)


title: HA only, replicate 1  [ha-1-inp-CGATGT_S1]


title: Day10-CD8-N-HA-2

first: David

middle: G

last: Gennert

address: 269 Campus Drive

department: Genetics

institute: Stanford University School of Medicine

data_processing:
Adapter sequences were trimmed by a custom Python script.
Reads were aligned to the hg19 genome by Bowtie2.
Duplicate reads were filtered by Picard, mitochondrial reads were removed, and reads were filtered for MAPQ quality scores ≥10.
Peaks were called with MACS2 using an FDR cutoff of 0.01.
Sequencing tracks were generated with the Washington University Epigenome Browser using read-number normalized BigWig files.
Differential peak analysis was carried out using DESeq2.
Transcription factor motif deviation analysis was carried out using chromVAR.
TF motif enrichment was calculated using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak files were generated for each ATAC-seq sample.

growth_protocol: Primary human T cells were isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies). Buffy coats were purchased from Stanford Blood Center and processed according to the manufacturer’s protocol using Lymphoprep density gradient medium and SepMate-50 tubes. Isolated T cells were cryopreserved at 2x107 T cells per vial in CryoStor CS10 cryopreservation medium (Stem Cell Technologies).  Cryopreserved T cells were thawed and activated same day with Human T-Expander CD3/CD28 Dynabeads (Gibco) at 3:1 beads:cell ratio in T cell media (AIMV supplemented with 5% FBS, 10mM HEPES, 2mM GlutaMAX, 100 U/mL penicillin, and 100ug/mL streptomycin (Gibco)). Recombinant human IL-2 (Peprotech) was provided at 100 U/mL.  T cells were transduced with retroviral vector on days 2 and 3 post activation and maintained at 0.5-1 x106 cells per mL in T cell media with IL-2. Non-tissue culture treated 12-well plates were coated overnight at 4C with 1mL Retronectin (Takara) at 25ug/mL in PBS. Plates were washed with PBS and blocked with 2% BSA for 15min. Thawed retroviral supernatant was added at ~1mL per well and centrifuged for 2 hours at 32C at 3200 RPM before the addition of cells. CAR T cells were used for in vitro assays on day 10-11 post activation.

extract_protocol:
100,000 cells from each sample were sorted by FACS into culture media, centrifuged at 500g at 4°C, then resuspended in ATAC-seq Resuspension Buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3mM MgCl2) supplemented with 0.1% NP-40,0.1% Tween-20, and 0.01% Digitonin.  Samples were split into two replicates each prior to all subsequent steps.  Samples were incubated on ice for 3 minutes, then washed out with 1 mL RSB supplemented with 0.1% Tween-20.  Nuclei were pelleted at 500g for 10 minutes at 4°C.
The nuclei pellet was resuspended in 50 μL transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (Illumina), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) and incubated at 37°C for 30 minutes in a thermomixer with 1000 RPM shaking.  The reaction was cleaned up using the Qiagen MinElute PCR Purification Kit. Libraries were PCR-amplified using the NEBNext Hi-Fidelity PCR Master Mix and custom primers (IDT) as described previously20. Libraries were sufficiently amplified following 5 cycles of PCR, as indicated by qPCR fluorescence curves20.  Libraries were purified with the Qiagen MinElute PCR Purification Kit and quantified with the KAPA Library Quantification Kit. Libraries were sequenced on the Illumina NextSeq at the Stanford Functional Genomics Facility with paired-end 75bp reads.

value: CAR T cell

tag: t cell type

tag: t cell memory

value: Naïve

tag: car target


title: Mac1cell_R18_C60

description: P1_Mac.txt (matrix)


title: JUN-HA, replicate 1  [jun-1-inp-ACAGTG_S4]

tag: genotype/variation


title: Phf21b_Input_N2A_Day2_Diff_Replicate1

description: ChIP-seq in N2A

tag: cell line


title: Day10-CD8-N-CD19-2

description: Day10_CD8_N_CD19_2_CGTACTAG_CTCCTTAC_S34


title: Day10-CD8-N-HA-1


title: Mac1cell_R18_C54

description: P1_Mac.txt (matrix)


title: Day10-CD8-N-CD19-1

description: Day10_CD8_N_CD19_1_TAAGGCGA_CTCCTTAC_S33


title: Mac1cell_R18_C53

description: P1_Mac.txt (matrix)


title: HA only, replicate 1  [ha-1-irf4-TTAGGC_S2]


title: Mac1cell_R18_C51

description: P1_Mac.txt (matrix)


title: HA only, replicate 1  [ha-1-jun-TGACCA_S3]


title: Day10-CD8-CM-HA-1

value: Central Memory


title: Mac1cell_R18_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R18_C2

description: P1_Mac.txt (matrix)


title: Day10-CD8-CM-CD19-2

description: Day10_CD8_CM_CD19_2_TAGGCATG_CTCCTTAC_S38


title: Day10-CD4-N-HA-2


title: Mac1cell_R18_C27

description: P1_Mac.txt (matrix)


title: Day10-CD4-N-HA-1


title: Day10-CD8-CM-CD19-1

description: Day10_CD8_CM_CD19_1_GGACTCCT_CTCCTTAC_S37


title: Mac1cell_R18_C34

description: P1_Mac.txt (matrix)


title: Day10-CD4-N-CD19-1

description: Day10_CD4_N_CD19_1_GTGTGGTG_TCTACTCT_S25


title: Day10-CD4-N-CD19-2

description: Day10_CD4_N_CD19_2_TGGGTTTC_TCTACTCT_S26


title: Mac1cell_R18_C23

description: P1_Mac.txt (matrix)


title: Mac1cell_R18_C22

description: P1_Mac.txt (matrix)


title: Day10-CD4-CM-HA-2


title: Mac1cell_R18_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R18_C16

description: P1_Mac.txt (matrix)


title: Mac1cell_R18_C19

description: P1_Mac.txt (matrix)


title: Day10-CD4-CM-CD19-2

description: Day10_CD4_CM_CD19_2_TTCCATAT_TCTACTCT_S30


title: si-con2

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Read count by homer (http://homer.salk.edu/homer/ngs/)
Genome_build: hg38
Supplementary_files_format_and_content: text files include mRNA molecule count values for each Sample

growth_protocol: cells were cultured in DME medium with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was isolated using Dynabeads mRNA Direct Kit (Thermo Fisher Scientific). NGS libraries were prepared using a modified version of Transeq, as described (Jaitin et al., 2014)
We used a derivation of the MARS-seq as described (Jaitin et al. Science 2014), developed for single cell MARS-seq to produce 3' exprssion libraries with a minimum of 3 replicates per sample.
3' RNA-seq for digital gene expression quantitation (single end protocol R2 used for 7N barcode + 8N UMI in fastq header)

treatment_protocol: Cells were transfected in triplicates with siRNA oligonucleotides (from Thermo Fischer Scientific) specific to FLI1, or with control oligonucleotides. Forty-eight hours later, cells were harvested and RNA was isolated

value: Ewing Sarcoma cell line

tag: transfected with

value: siRNA -scrambeled (si-con)

tag: selection markers

value: EWS-FLI1 fusion


title: Mac1cell_R18_C10

description: P1_Mac.txt (matrix)


title: Day10-CD4-CM-CD19-1

description: Day10_CD4_CM_CD19_1_CGCGGACA_TCTACTCT_S29

tag: cell type


title: Day10-CD8-CM-HA-2


title: Day10-CD4-CM-HA-1


title: Mac1cell_R17_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C65

description: P1_Mac.txt (matrix)


title: si-FL13

value: siRNA-FLI1 oligonucleotide


title: Mac1cell_R17_C58

description: P1_Mac.txt (matrix)

value: Retina


title: si-con1


title: Mac1cell_R17_C62

description: P1_Mac.txt (matrix)


title: si-FL11


title: si-FL12


title: Mac1cell_R17_C57

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C53

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C52

description: P1_Mac.txt (matrix)


title: si-con3


title: Mac1cell_R17_C3

description: P1_Mac.txt (matrix)


title: 57_Wild type, TNFa at 30 ng/mL, 4h

first: Paul

last: Blainey

address: 415 Main Street

institute: Broad Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Transcript counts were quantified using the command "kallisto quant" with default parameters and human reference Homo_sapiens.GRCh37.75.cdna.abinitio.fa.gz (kallisto v0.45).
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Transcript counts determined by kallisto are stored in a tab-delimited table with one row per transcript feature.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100U/mL penicillin/streptomycin

extract_protocol:
Cells were washed once with PBS and lysed in 1X TCL buffer (Qiagen, supplemented with 1% beta-mercaptoethanol).
Smart-seq2 was performed as described (Trombetta et al., 2014).

treatment_protocol: Cytokines were added directly to culture media.

value: HeLa

value: wt

tag: stimulation

value: TNF 1/3k

tag: timepoint

tag: clone


title: 96_Wild type, unstimulated

value: unstimulated


title: 38_Wild type, unstimulated


title: 7_Wild type, TNFa at 30 ng/mL, 4h


title: 1_Wild type, TNFa at 30 ng/mL, 4h


title: Mac1cell_R17_C37

description: P1_Mac.txt (matrix)

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
Single nuclear capture and sequencing were performed on the ICELL8 single cell platform (Wafergen Biosytems). ICELL8 platform comprised of a multi-sample nano-dispenser that precisely dispensed 50nl of the single nuclei suspension into an ICELL8 nanowell microchip-containing 5184 wells (150nl capacity). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy of the microchip was performed using an Olympus BX43 fluorescent microscope with a robotic stage to visualize wells containing single nuclei (see Table 1 for single cell capture number across different experimental repeats). The automated well selection was performed using the CellSelect software (Wafergen Biosystems), which identified nanowells containing single nuclei and excluded wells with >1 nuclear, debris, nuclei clumps or empty wells. The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multi-sample nano-dispenser to candidate wells. Each well had a preprinted primer that contains an 11-nucleotide-well-specific barcode. This barcode was added to the 3’ (A)n RNA tail of the nuclear transcripts during reverse transcription and cDNA amplification, the latter of which was performed on candidate wells using SCRB-seq chemistry. After RT, the cDNA products from candidate wells were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified using 0.6x AMPure XP beads. A 3’ transcriptome enriched library was made using Nextera XT Kit and 3’-specific P5 primer, which was sequenced on the Illumina Hiseq2500.

tag: sample

tag: tissue


title: 31_Wild type, TNFa at 30 ng/mL, 1h


title: 25_Wild type, TNFa at 30 ng/mL, 1h


title: Mac1cell_R17_C40

description: P1_Mac.txt (matrix)


title: 19_Wild type, TNFa at 1 ng/mL, 4h


title: Mac1cell_R17_C36

description: P1_Mac.txt (matrix)


title: 69_Wild type, TNFa at 1 ng/mL, 4h


title: 37_Wild type, TNFa at 1 ng/mL, 1h


title: Mac1cell_R17_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R17_C13

description: P1_Mac.txt (matrix)


title: 43_Wild type, TNFa at 1 ng/mL, 1h


title: Mac1cell_R17_C22

description: P1_Mac.txt (matrix)


title: 13_Wild type, TNFa at 1 ng/mL, 4h


title: 44_Wild type, unstimulated


title: Mac1cell_R16_C69

description: P1_Mac.txt (matrix)


title: 93_Wild type, TNFa at 1 ng/mL, 1h


title: Mac1cell_R17_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C64

description: P1_Mac.txt (matrix)


title: 58_Wild type, IL-1b at 30 ng/mL, 4h


title: 8_Wild type, IL-1b at 30 ng/mL, 4h


title: Mac1cell_R16_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C5

description: P1_Mac.txt (matrix)


title: 26_Wild type, IL-1b at 30 ng/mL, 1h


title: 32_Wild type, IL-1b at 30 ng/mL, 1h


title: 82_Wild type, IL-1b at 30 ng/mL, 1h


title: 2_Wild type, IL-1b at 30 ng/mL, 4h


title: 20_Wild type, IL-1b at 1 ng/mL, 4h


title: 14_Wild type, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R16_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C44

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C7

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R16_C28

description: P1_Mac.txt (matrix)


title: 88_MED24 knockout, unstimulated


title: 46_MED24 knockout, unstimulated


title: Mac1cell_R16_C24

description: P1_Mac.txt (matrix)


title: 51_MED24 knockout, TNFa at 30 ng/mL, 4h


title: Mac1cell_R16_C60

description: P1_Mac.txt (matrix)


title: 86_MED24 knockout, unstimulated

value: MED24 KO 2.1


title: Mac1cell_R16_C1

description: P1_Mac.txt (matrix)


title: 49_MED24 knockout, TNFa at 30 ng/mL, 4h


title: Mac1cell_R16_C19

description: P1_Mac.txt (matrix)


title: 11_MED24 knockout, TNFa at 30 ng/mL, 4h


title: Mac1cell_R16_C14

description: P1_Mac.txt (matrix)


title: 9_MED24 knockout, TNFa at 30 ng/mL, 4h


title: Mac1cell_R16_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C69

description: P1_Mac.txt (matrix)


title: 70_Wild type, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R15_C57

description: P1_Mac.txt (matrix)


title: 33_MED24 knockout, TNFa at 30 ng/mL, 1h


title: 75_MED24 knockout, TNFa at 30 ng/mL, 1h


title: 73_MED24 knockout, TNFa at 30 ng/mL, 1h


title: Mac1cell_R15_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C45

description: P1_Mac.txt (matrix)


title: 35_MED24 knockout, TNFa at 30 ng/mL, 1h


title: 48_MED24 knockout, unstimulated


title: Mac1cell_R15_C40

description: P1_Mac.txt (matrix)


title: 63_MED24 knockout, TNFa at 1 ng/mL, 4h


title: 23_MED24 knockout, TNFa at 1 ng/mL, 4h


title: Mac1cell_R15_C43

description: P1_Mac.txt (matrix)


title: 21_MED24 knockout, TNFa at 1 ng/mL, 4h


title: 61_MED24 knockout, TNFa at 1 ng/mL, 4h


title: Mac1cell_R15_C28

description: P1_Mac.txt (matrix)


title: 45_MED24 knockout, TNFa at 1 ng/mL, 1h


title: 87_MED24 knockout, TNFa at 1 ng/mL, 1h


title: Mac1cell_R15_C2

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C30

description: P1_Mac.txt (matrix)


title: 85_MED24 knockout, TNFa at 1 ng/mL, 1h


title: Mac1cell_R15_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C66

description: P1_Mac.txt (matrix)