April 2008

ATACseqQC for quality assessment of ATACseq dataset July 26th 2017 NADfinder for identifying Nucleoli Associated Domain (NAD)

Lihua Julie Zhu and Jianhong Ou Assay for Transposase- Accessible Chromatin using Sequencing (ATAC-seq)

Adapted from Nature Methods 10, 1213–1218, 2013 By Buenrostro and Greenleaf et al. ATACseqQC Package • Provide quick assessment of the quality of the ATAC-seq data – diagnostic plot of insert size distribution of sequenced fragments (periodicity) – proportion of mitochondria reads (< 5%) – genome-wide nucleosome positioning pattern at TSS – CTCF or other Transcript Factor footprints (depleted signals)

Adapted from Nature Methods 10, 1213–1218, 2013 By Buenrostro and Greenleaf et al. Expected patterns of nucleosome occupancy and depletion at the TSS Density Plot Flanking TSS

- Nucleosome free -- Nucleosome bound Generate footprints for DNA-binding NADFINDER NUCLEOLI ARE THE LARGEST NUCLEAR BODIES AND ARE SURROUNDED BY HETEROCHROMATIN

http://schoolbag.info/chemistry/mcat_biochemistry/mcat_ van Koningsbruggen et al… Lamond, MBoC 2010 biochemistry.files/image140.jpg NADfinder Workflow ZK1248.17 Bioconductor Packages By MCCB Y69E1A.5 Y59E9AL.3

F44A2.5

clec-66 scl-27 hpd-1 msp-76 K10C2.3 mir-239.1 mir-72 hpo-28 mir-76

htas-1 F01D5.3 F35H8.4 mir-242

nhr-86 F32A5.4 K09H11.7 mir-63 R10H10.3 C08E8.3 msp-51 Y106G6A.4 T05E12.6 F57G8.7 srd-16 mir-228 F55G11.7 T01D3.6 C02F5.5 dod-24 bre-1 mir-52 lsy-2 C33F10.1 mbf-1 C01B10.4 C17A2.4 mir-73 sss-1

Y37D8A.5mir-229 mir-788 th K03H1.12 mir-43 mir-240 mir-53 mir-75 mir-46 C33D9.9 cdh-5 F01D5.1 mir-2 • Workshop By J Ou and LJ Zhu on July 28 , 3:15 - 5:00 Smith 309 mir-74 T11B7.5 C50F4.9 clec-76 pos-1 sre-13 Y49G5A.1 T22B7.7 mir-230 scd-1 lnp-1 T05C3.6 mig-5 lin-4 msp-63 ssq-2 Y54G11A.14 daf-12 pdi-2 mir-84 K10D3.6 msp-50 F21C10.11 ces-2 C36C9.1 col-172 mir-237 ugt-6 let-7 mir-261 clec-52 msp-142 mir-87 nhr-42 nhr-20 atf-6 daf-3 pho-1 F11G11.4 msp-56 zip-2 mir-241 T01B11.2 pho-12 W01B6.4 lin-13 mir-795 mir-44 B0507.10 nhr-1 fli-1 mir-243 nspd-10 C27F2.7 mir-42 mir-41 Y40C5A.1 F09F7.4 – ChIPpeakAnno (BMC Bioinformatics 2010) grd-10 nhr-10 tbc-7 mir-80 mir-355 mir-37 ceh-45 mir-35 mir-1 clec-4 K12H4.7 gst-27 F36D1.4 C27D6.3 mir-40 C12D5.4 mir-38 hlh-30 mir-51 meg-2 mir-36 C24B9.3 col-19 gst-11 wago-9 mir-39 Y44A6D.1 F35E12.5 mir-58 col-20 C32H11.4 nspd-1 grd-5 fut-1 dyc-1 ilys-2 cyp-14A5 Y67A6A.1

Y75B8A.23 – GeneNetworkBuilder mir-34 far-3

W10C8.5 C53A5.2 – TrackViewer msp-38 • Workshop by LJ Zhu on July 27th , 1-2:45pm Smith 309 – CRISPRseek (PLoS One 2014)

– GUIDEseq (BMC Genomics 2017)

MEOX2 2 MEOX2 so HNF1B 1 HNF1B Optix

HNF1A Six4

HNF1B VENTX 1

HOXD8 VENTX

EVX2 ● ● ● ● Otx1 2

EVX1 ● ● ● ● ● OTX1

onecut ● ● ● OTX2

CG7056 ● ● RHOXF1 1 CG13424 ●

● ● ● RHOXF1 1 repo ● DPRX C15 ●

● ● RHOXF1

CG12361 ● ● RHOXF1

abd A abd ● ● DPRX 1

Ubx ● ● OTX2 1

HGTX ● ● Otx1 3

NKX6 1 NKX6 ● oc

● ●

DLX1 bcd

● ●

ALX3 ● ● Ptx1

MIXL1 ● ● PITX1 1

HOXA1 ●

● OTX1 1

Lhx8 1 Lhx8 ●

● PITX3

LMX1B ●

● PITX1

Prrx2 ● ● PITX1 Lim3 ●

● GSC

● en ● Gsc Dr ●

● DMBX1

●

exex ● GSC2

inv ● ● Hoxd9 OdsH ●

● HOXC10

●

unc 4 unc ● HOXD11 1

●

slou ● HOXC11 1 ●

unpg ● HOXD12

●

Lim1 ● HOXC12

●

CG33980 ● Hoxc10 4

●

CG32105 ● Hoxd9 1

●

CG4328 ● HOXC11 1

●

CG32532 ● Hoxd13 2

●

CG4136 ● HOXD13

●

hbn ● HOXC13

●

CG11294 ● HOXA13

●

ro ● HOXB13 ●

ap ● HOXA13

●

E5 ● CDX2

●

CG9876 ● CDX1

●

Rx ● cad

●

otp ● Abd B ●

• NADFinder (Poster) Pph13 ●

HOXC10 1 ●

VAX1 ● HOXD12 3 ●

Lhx4 ● HOXA10 1 ●

LMX1A ● H2 0 ●

Alx1 ● Hoxa11 1 ●

ALX3 ● Hoxd9 2 ●

MNX1 ● HOXD12 2 ●

EMX1 ● Hoxc10 3 ●

Hoxd3 ● HOXC10 2 ●

HOXB5 ● HOXC11 ●

HOXB3 ● HOXD11 ●

GSX1 ● HOXC11 ●

GSX2 ● HOXD12 1 ●

Hoxa2 1 Hoxa2 ● HOXC12 1 ●

HOXB2 ● Hoxa11 ●

HOXA2 ● HOXA10 ●

lbe ● HOXB13 1 ●

lbl ● HOXA13 1 ●

Meox2 3 Meox2 ● HOXD13 1 ●

ftz ● HOXC13 1 ●

ems ● HOXA13 1 ●

lab ● Hoxd13 3 ●

zen2 ● BARHL2 ●

CG18599 ● Barhl1 ●

●

pb BARHL2 ●

zen ● ct ●

●Dfd mirr

●caup ●

Antp ● ●

●Scr CG11617 ●

●bsh ara ●

●btn Rhox11 ●

NKX6 1 ●NKX6 hth ●

PDX1 1 ●PDX1 achi ●

Nkx6 1 1 1 ●Nkx6 vis ●

NKX6 2 ●NKX6 exd ●

NKX6 2 ●NKX6 IRX5 ●

●MEOX2 IRX2 ●

●EMX2 Irx3 ●

En2 1 ●En2 NKX3 2 • ATACseqQC ●

●VSX1 ISL2 ●

●LHX2 NKX3 1 ●

●NOTO Nkx3 1 ●

●LHX6 NKX2 8 ●

●Ind NKX2 8 ●

●VAX2 NKX2 3 ●

●Awh NKX2 3 ●

●

eve vnd ●

●al tin ●

Uncx 3 ●Uncx EN1 1 ●

●VSX1 EN1 1 ●

●VSX2 GBX2 1 ●

LHX2 1 ●LHX2 EMX2 1 ●

MEOX2 1 ●MEOX2 EMX1 1 ●

●LBX2 Lag1 ●

●MEOX1 HMBOX1 ●

●Dll LHX9 1 ●

●DUXA

● HESX1 1

●ALX4

● MSX1

Alx4 1 ●Alx4

● BARX1

Alx1 1 ●Alx1

● MSX2

●PROP1

● Msx3

●PROP1

● Lhx8 2

●PHOX2B

● LHX6 2

●PHOX2B

● Lhx8

ALX3 1 ● ALX3

● LHX6 1

● PHOX2A

● PDX1

● ARX

● BARHL2 2

Arx 1 ● Arx

● Barhl1 2

● UNCX

● BARHL2 2

Uncx 2 ● Uncx

● Gbx1 1

● ISX

● PHDP

● DRGX

● HESX1

● CART1

● Gbx2 2

PRRX1 1 ● PRRX1

● GBX2 ● HMX3

● EN1

●

Bap ● LBX2 1

● HMX2

● RAX ● HMX1

● UNCX 1

●

tup ● PRRX1

● CG34031 ● EN1

● Hmx ● Shox2 1

Barhl1 1 ● Barhl1 ● SHOX

BARHL2 1 ● BARHL2 ● ISX

BARHL2 1 ● BARHL2 ● DLX5

● EN2 ● LMX1B

● GBX2 ● Vsx1 1

BARX1 1 ● BARX1 ● SHOX2

● BSX ● RAXL1

●H1 B ● PRRX1

●H2 B ● DLX6

● CG11085 ● Dlx1 1

● DLX2 ● Dlx2 1

●1 MSX2 ● PRRX2

● MSX1 ● NK7 1

●1 MSX1 CG15696

● 1 Msx3 DLX4 ●

EN2 ●

DLX3 ● GBX1 ISX 1 • cleanUpdTseq (Bioinformatics 2013) ● ● LHX9 ● ● • REDseq (BMC Genomics 2014 ) • MotifStack (in prep) • InPAS • dagLogo Acknowledgement

• University of Massachusetts Medical School • Broad Institute of MIT and Harvard • Feng Zhang (CRISPRseek) – Usha Acharya & Niraj Nirala (dagLogo) – Benjamin Holmes – Neil Aronin (CRISPRseek) • Genentech – Michael Brodsky (CRISPRseek & MotifStack) - Michael Lawrence(GUIDEseq) – Tom Fazio and Benson Chen (REDseq) • The Bioconductor core members – Claude Gazin & Chris Hull (ChIPpeakAnno) – Hervé Pagès (ChIPpeakAnno, – Michael Green (ChIPpeakAnno & InPAS) CRISPRseek & GUIDEseq) – Alper Kucukural & Manuel Garber (GUIDEseq) – Martin Morgan (CRISPRseek) – Nathan Lawson (ChIPpeakAnno, ATACseqQC & cleanUpdTSeq) – Valerie Obenchain – Jianhong Ou (ChIPpeakAnno, dagLogo, NADfinder, ATACseqQC, – Dan Tenenbaum GeneNetworkBuilder, MotifStack, TrackViewer, InPAS) • The Bioconductor community – Sungmi Park ( InPAS) Lucio Castilla (ATACseqQC) • Ryan Thompson (ChIPpeakAnno) – Sarah Sheppard (cleanUpdTSeq) Paul Kaufman (NADfinder) • Nationwide Children's Hospital – Heidi Tissenbaum (GeneNetworkBuilder) • Simon Lin (ChIPpeakAnno) – Yongxu Wang (TrackViewer) Michelle Kelliher (ATACseqQC) • Tufts University – Scot Wolfe (GUIDEseq and motifStack) • David Lapointe (ChIPpeakAnno) – Jun Yu (ChIPpeakAnno, NADfinder, ATACseqQC)