README_template.md

README_template

Description: CITE-seq of HSPC and Mature bone marrow mononuclear cells in Scl-Cre SRSF2 P95H mutant vs WT mice

2023_06_23

Summary

This project seeks to understand how ... using the model ... for the purpose of ...

Contributors

Name, role...

Sample prep

Basic Info

Category	Info
Organism	Black 6 mouse
Tissue	Bone Marrow
Genetic Modification	Scl-Cre SRSF2 P95H
Sex	Female
Molecule	Total RNA
Single or paired-end	paired
Instrument model	NovaSeq
Targeted cells / channel	20K
Expected read length	150

Subjects

Subject ID	Genotype
1880	WT
1881	WT
1982	P95H mut
1983	P95H mut

Cells

FACS sorted Bone marrow populations:

1. HSPC: DAPI (-), mCD45 (+), cKit(CD117) (+), tdTomato (+)
2. Mature: DAPI (-), Ter119 (-), mCD45 (+), tdTomato (+)

CITE ADTs

[CD4, CD8a, Ly-6C, CD11b, Ly-6G, CD44, CD19, CD135, CD16/32, Sca1, CD201, B220, CD115, CD11c, CD62L, F4/80, I-A/I-E, CD127, CD150, CD48, NK1.1, CD3, CD27, CCR2, CX3CR1, CD41, CD34]

Hashing

Subject ID	Compartment	Hash
1880	HSPC	1
1881	HSPC	2
1982	HSPC	3
1983	HSPC	4
1880	Mature	5
1881	Mature	6
1982	Mature	7
1983	Mature	8

Library prep

Notes: Samples were pooled after hashing, then run on two separate channels in the 10X controller.

Protocol: Chromium Next GEM Single Cell 3' Reagent Kits, Dual Index (v3.1 Chemistry)

Kit(CAT):

1. Chromium Next GEM Single Cell 3' Kit v3.1, 4 rxns (PN-1000269)
2. 3' Feature Barcode Kit (PN-1000262)
3. Dual Index Kit TT Set A (PN-1000215)
4. Dual Index Kit NT Set A (PN-1000242)
5. Chromium Next GEM Chip G Single Cell Kit, 16 rxns (PN-1000127)

Libraries

Sample naming convention: compartment_subjectID_genotype_10Xchannel

Library Name
HSPC_1880_WT_1
HSPC_1881_WT_1
HSPC_1982_P95H_1
HSPC_1983_P95H_1
Mature_1880_WT_1
Mature_1881_WT_1
Mature_1982_P95H_1
Mature_1983_P95H_1
HSPC_1880_WT_2
HSPC_1881_WT_2
HSPC_1982_P95H_2
HSPC_1983_P95H_2
Mature_1880_WT_2
Mature_1881_WT_2
Mature_1982_P95H_2
Mature_1983_P95H_2

Analysis

Data locations

Raw:

...

Preprocessed (ie. CellRanger):

...

Downstream:

...