Miscellaneous

Contributors

Contributors, listed alphabetically: Sarah Aufmkolk, Bogdan Bintu, Alistair Boettiger, Andrea Cosolo, Adam Jussila, Caterina Strambio De Castillia, Steven Wang.

Older revision history

Note

Older versions of this document are available in the following Google Doc: https://docs.google.com/document/d/1z7rIYsQnbeS7y_SMuwoa8qsWKBD_BpV88vR79WiH_XI/edit?usp=sharing and Google Sheet: https://docs.google.com/spreadsheets/d/1GvqokS5w8Yw2tAngsqDC8YcLdRha5cGr/edit?usp=sharing&ouid=103316056144222958298&rtpof=true&sd=true

Feb 1, 2021 Alistair Boettiger

Feb 2, 2021 Bogdan Bintu, Steven Wang, Alistair Boettiger

Feb 8, 2021 Bogdan Bintu, Steven Wang, Alistair Boettiger

Feb 9, 2021 Steven Wang, Andrea Cosolo, Andrew Schroeder, Alistair Boettiger

Feb 12, 2021 Alistair

Feb 26, 2021 Caterina Strambio De Castillia

July 6, 2021 Alistair, Andrea

Aug, 2021, Sarah + Alistair

Sept 10, 2021 Alistair

Sept 16, 2021 Sarah (addition of SMLM data example #3 and #4)

October 18-29, 2021 Caterina (various comments and changes)

October 25, 2021 Discussion between Alistair and Caterina to address several comments/issues. The main clarification point was that this format is used specifically to define Chromatin Tracing results. This is a subtype of a more generic FISH Omics Format. Other subtypes will be defined ASAP.

November, 2021 Caterina (various comments and changes)

February 9, 2022 Caterina and Andrea: Change name and description for tables #4 and #5 and add Table# to table header.

4DN Experimental and Microscopy Metadata

  • Project =

  • Center =

  • Lab =

  • Experiment protocol description =

  • Date collected =

  • Date submitted =

  • Experiment Type = FISH Omics - Chromatin Tracing

  • Experiment Set Type = Replicate

  • Organism = D. melanogaster

  • Biosource Type = tissue culture cell line

  • Biosource = IMR90

  • Modification Type = none

  • Treatment Type = none

  • Microscopy Metadata (including Provenance and Quality Control) conforming to 4DN-BINA-OME data model

  • Browsable probe map, (bed file, see example)

  • Probe sequences, (fasta file, see example)

Useful information

OME-NGFF and OME-Zarr

Browsable probe map, example bed file

track name="AllRegions" description="mm10 AllRegions" visibility=1 itemRgb="On"
chr12 113100000 113130000 IgH_001 1 + 113100000 113130000 255,0,0
chr12 113130001 113160001 IgH_002 1 + 113130001 113160001 255,14,0
chr12 113160002 113190002 IgH_003 1 + 113160002 113190002 255,28,0
chr12 113190003 113220003 IgH_004 1 + 113190003 113220003 255,42,0
...

Probe sequence, example fasta file

>FwdPrimer01__BarcodeName__SecondBarcodeName__probeTargetName_p001__RevPrimer01
GCGGGACGTAAGGGCAACCGcatcaacgccacgatcagctGCTATCGTTCGTTCGAGGCCaggcaattcgagtggcgccctcgaagacgtctcgcaccttCCGTTCTGAGGGTTGCCGTG
>FwdPrimer01__BarcodeName__SecondBarcodeName__probeTargetName_p002__RevPrimer01
GCGGGACGTAAGGGCAACCGcatcaacgccacgatcagctGCTATCGTTCGTTCGAGGCCagactttggaagccaccctcattgattgctcgtgctccatCCGTTCTGAGGGTTGCCGTG
...

Example published / available data sets

  • Wang…Zhuang 2016, Science (IMR90)

  • Bintu,Mateo…Boettiger,Zhuang, 2018, Science (IMR90, K562, A549, HCT116)

  • Mateo…Boettiger 2019, Nature (mESC + D. mel)

  • Liu…Wang 2020, Nat. Com. (mouse liver)

  • Saw…Wang,Mango 2020, Mol Cell (C. elegans)

  • Su…Bintu,Zhuang 2020 Cell (IMR90)

  • Takei…Cai 2021 Nature (mESC)

  • Takei…Cai 2021 bioRxiv (mouse brain)

  • Wiggins…Boettiger,Crabtree. 2021 NSMB, (mESC)

Example Tables

[Other publications with potentially accessible and similar data to aggregate]