|
| Status |
Public on Feb 28, 2022 |
| Title |
E9.5_embryo_puck_201104_32 |
| Sample type |
SRA |
| |
|
| Source name |
E9.5 embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: E9.5 embryo
strain: B6D2F1xCAST
genotype: WT
section: saggital
cross: B6D2F1 (F1 oocyte) x CAST sperm
treatment: mock electroporated
|
| Treatment protocol |
Zygotes electroporated with Cas9-RNP with guides targeting GFP (mock)/Tbx6 (Tbx6 KO)
|
| Growth protocol |
Pre-implantation embryos were cultured in standard embryo media. In brief, 25uL of KSOM media drops were added to the petridish and covered with mineral oil. The culture dish with KSOm was pre-gassed prior to transfer of embryos. Embryos were re-transferred bilaterally to uetrine horn of pseudopregnant 2.5dpc surrogate CD1 female mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Slide-seq v2
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
wild type embryos from in vitro fertilized zygotes - saggital section
|
| Data processing |
Library strategy: Spatial Transcriptomics
Base-calling from images was performed by a custom MATLAB package ArrayCaller (https://github.com/MacoskoLab/ArrayCaller/).
The sequenced reads were processed by Slide-seq tools pipeline (https://github.com/MacoskoLab/slideseq-tools) to generate the gene count matrix and match bead barcode between array and sequenced reads.
Genome_build: mouse GRCm38.81
Supplementary_files_format_and_content: XXX.digital_expression.txt.gz is the gene count matrix where the rows are genes and columns are beads. XXX_matched_bead_location.txt is the bead spatial location file where the rows are in the order as XXX.digital_expression.txt.gz. Read1 contains the transcript sequence and Read2 contains bead barcode (14bp) followed by bead UMI sequence (8bp). puck_rawimage_XXX.tar contains the raw image from puck sequencing, which is used to obtain the spatial location of the bead barcodes.
|
| |
|
| Submission date |
Feb 24, 2022 |
| Last update date |
Mar 05, 2022 |
| Contact name |
Luyi Tian |
| E-mail(s) |
ltian@broadinstitute.org
|
| Phone |
8577779729
|
| Organization name |
Broad institute
|
| Lab |
Fei Chen Lab
|
| Street address |
415 main st Cambridge
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE197353 |
Spatial transcriptomic maps of whole mouse embryos |
|
| Relations |
| BioSample |
SAMN26226157 |
| SRA |
SRX14276871 |
