April 2008

Lihua Julie Zhu and Jianhong Ou

ATACseqQC for quality assessment of ATACseq datasetNADfinder for identifying Nucleoli Associated Domain (NAD)

July 26th 2017

Adapted from Nature Methods10, 1213–1218, 2013By Buenrostro and Greenleaf et al.

Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq)

• 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)

ATACseqQC Package

Adapted from Nature Methods 10, 1213–1218, 2013By 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 proteins

NADFINDERNUCLEOLI ARE THE LARGEST NUCLEAR BODIES AND

ARE SURROUNDED BY HETEROCHROMATIN

van Koningsbruggen et al… Lamond, MBoC 2010http://schoolbag.info/chemistry/mcat_biochemistry/mcat_biochemistry.files/image140.jpg

NADfinderWorkflow

• Workshop By J Ou and LJ Zhu on July 28th, 3:15 - 5:00 Smith 309

– ChIPpeakAnno (BMC Bioinformatics 2010)

– GeneNetworkBuilder

– TrackViewer

• Workshop by LJ Zhu on July 27th , 1-2:45pm Smith 309

– CRISPRseek (PLoS One 2014)

– GUIDEseq (BMC Genomics 2017)

• NADFinder (Poster)

• ATACseqQC

• cleanUpdTseq (Bioinformatics 2013)

• REDseq (BMC Genomics 2014 )

• MotifStack (in prep)

• InPAS

• dagLogo

ctBARHL2Barhl1BARHL2Hoxd13 3HOXA13 1HOXC13 1HOXD13 1HOXA13 1HOXB13 1HOXA10Hoxa11HOXC12 1HOXD12 1HOXC11HOXD11HOXC11HOXC10 2Hoxc10 3HOXD12 2Hoxd9 2Hoxa11 1

H2 0HOXA10 1HOXD12 3

HOXC10 1Abd BcadCDX1

CDX2HOXA13

HOXB13HOXA13

HOXC13

HOXD13

Hoxd1

3 2

HOXC11 1

Hoxd9

1

Hoxc1

0 4

HOXC12

HOXD12

HOXC11

1

HOXD11

1

HOXC10

Hoxd

9

GSC2

DMBX

1

Gsc

GSC

PITX

1PI

TX1

PITX

3OT

X1 1

PITX

1 1

Ptx1bcd

ocOtx

1 3

OTX2

1DP

RX 1

RHOX

F1RH

OXF1

DPRX

RHOX

F1 1

RHOX

F1 1

OTX

2O

TX1

Otx

1 2

VEN

TXVE

NTX

1Si

x4O

ptix

soMEO

X2 2

HN

F1B

1H

NF1

AH

NF1

BH

OXD

8EV

X2EV

X1on

ecut

CG70

56CG

1342

4re

poC1

5CG

1236

1ab

d A

Ubx

HGTX

NKX6

1DL

X1AL

X3M

IXL1

HOXA

1Lh

x8 1

LMX1

BPr

rx2

Lim3

enDrexex

invOdsH

unc 4

slou

unpg

Lim1

CG3398

0

CG3210

5

CG4328

CG3253

2

CG4136

hbnCG11294

roapE5CG9876

RxotpPph13VAX1Lhx4LMX1AAlx1ALX3MNX1EMX1Hoxd3HOXB5HOXB3GSX1GSX2Hoxa2 1HOXB2HOXA2lbelblMeox2 3ftzems lab zen2 CG18599pbzen Dfd Antp Scr bsh btn NKX6 1 PDX1 1 Nkx6 1 1 NKX6 2 NKX6 2 MEOX2 EMX2 En2 1 VSX1 LHX2 NOTO LHX6 Ind VAX2 Awh eve al Uncx 3 VSX1 VSX2 LHX2 1

MEOX2 1LBX2 MEOX1

Dll DUXAALX4

Alx4 1Alx1 1

PROP1

PROP1

PHOX2B

PHOX2B

ALX3 1

PHOX2A

ARX Arx 1UNCXUncx 2

ISX DRGXCART1

PRRX1 1

HMX3

BapHM

X2HM

X1tup CG

34031

Hmx

Barhl1 1BARHL2 1

BARHL2 1

EN2G

BX2BARX1 1BSXB H1B H2CG

11085DLX2M

SX2 1M

SX1M

SX1 1M

sx3 1EN

2G

BX1LH

X9ISX 1D

LX3D

LX4C

G15696

NK7 1PRRX2Dlx2 1Dlx1 1DLX6PRRX1RAXL1SHOX2Vsx1 1LM

X1BDLX5ISXSHOXShox2 1EN1PRRX1UNCX 1

RAXLBX2 1

EN1GBX2

Gbx2 2HESX1

PHDPGbx1 1

BARHL2 2

Barhl1 2BARHL2 2

PDX1LHX6 1

Lhx8

LHX6 2

Lhx8 2

Msx3MSX2

BARX1

MSX1

HESX1 1

LHX9 1

HMBOX1

Lag1EMX1 1

EMX2 1

GBX2 1

EN1 1EN1 1tinvndNKX2 3NKX2 3NKX2 8NKX2 8Nkx3 1NKX3 1ISL2NKX3 2Irx3IRX2IRX5exdvisachihthRhox11araCG11617caupmirr

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C02F5.5

mi r -46C33D9.9

C01B10.4

mi r -52

mi r -53

C17A2.4

mi r -228

F01D5.1

srd-16

mb f - 1

mi r -74

mi r -229Y37D8A.5

lsy-2

mi r -75

C50F4.9

mi r -73

hpd -1

F32A5.4

C08E8.3

K10C2.3

Y69E1A.5

mi r -76

htas-1

Y59E9AL.3

dod-24

R10H10.3

sss-1

mi r -240

K09H11.7

pos-1

mi r -43

F55G11.7T01D3.6

cdh-5

T05E12.6

mi r -788

F57G8.7

C33F10.1

F01D5.3

K03H1.12

scl-27

m i r - 2

mi r -242

bre-1

mi r -63nhr -86

hpo-28

Y106G6A.4

F35H8.4

msp-51

clec-66

mi r -72

F44A2.5

ZK1248.17

msp-76

mir-239.1

mi r -87

B0507.10

T11B7.5

pho-1

clec-52

f l i - 1

T05C3.6

nspd-10

Y54G11A.14F21C10.11

Y49G5A.1

F36D1.4

K10D3.6

C27F2.7

nspd-1

ceh-45

meg-2

col-172

z ip -2

tbc -7

mi r -230

wago-9col -19

m i r - 1clec-4

g rd -5

gst -11

dyc-1

nhr -20

T22B7.7

F35E12.5

mi r -243

mi r -44

m ig -5

mi r -80

nhr -42

h lh-30

mi r -40

C24B9.3

i lys-2

mi r -58Y44A6D.1

Y75B8A.23

gst -27

cyp-14A5

col-20

C53A5.2

mi r -34far -3

msp-38

Y67A6A.1

W10C8.5

nhr -10

a t f -6

W01B6.4

ces-2mi r -237

l i n -4

nh r -1

daf -12

grd-10

C12D5.4

F09F7.4

mi r -84

sre-13lnp -1

msp-56

mi r -261

pho-12 T01B11.2

C36C9.1

mi r -42

msp-142le t -7

mi r -795

mi r -37

ug t -6

F11G11.4

ssq-2msp-63

C27D6.3

mi r -51

clec-76

msp-50

fu t - 1

mi r -39

Y40C5A.1

mi r -355

pd i -2

mi r -38

daf -3

mi r -41

l in -13mi r -241

mi r -35

mi r -36

scd-1

C32H11.4

K12H4.7

Bioconductor Packages By MCCB

• University of Massachusetts Medical School– Usha Acharya & Niraj Nirala (dagLogo)

– Neil Aronin (CRISPRseek)

– Michael Brodsky (CRISPRseek & MotifStack)

– Tom Fazio and Benson Chen (REDseq)

– Claude Gazin & Chris Hull (ChIPpeakAnno)

– Michael Green (ChIPpeakAnno & InPAS)

– Alper Kucukural & Manuel Garber (GUIDEseq)

– Nathan Lawson (ChIPpeakAnno, ATACseqQC & cleanUpdTSeq)

– Jianhong Ou (ChIPpeakAnno, dagLogo, NADfinder, ATACseqQC, GeneNetworkBuilder, MotifStack, TrackViewer, InPAS)

– Sungmi Park ( InPAS) Lucio Castilla (ATACseqQC)

– Sarah Sheppard (cleanUpdTSeq) Paul Kaufman (NADfinder)

– Heidi Tissenbaum (GeneNetworkBuilder)

– Yongxu Wang (TrackViewer) Michelle Kelliher (ATACseqQC)

– Scot Wolfe (GUIDEseq and motifStack)

– Jun Yu (ChIPpeakAnno, NADfinder, ATACseqQC)

• Broad Institute of MIT and Harvard

• Feng Zhang (CRISPRseek)

– Benjamin Holmes

• Genentech

- Michael Lawrence(GUIDEseq)

• The Bioconductor core members

– Hervé Pagès (ChIPpeakAnno, CRISPRseek & GUIDEseq)

– Martin Morgan (CRISPRseek)

– Valerie Obenchain

– Dan Tenenbaum

• The Bioconductor community

• Ryan Thompson (ChIPpeakAnno)

• Nationwide Children's Hospital

• Simon Lin (ChIPpeakAnno)

• Tufts University

• David Lapointe (ChIPpeakAnno)

Acknowledgement