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. 2024 May 21;5(6):101576. doi: 10.1016/j.xcrm.2024.101576
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Rabbit Polyclonal anti-KRT6A Proteintech Cat# 10590-1-AP; RRID: AB_2134306
Rabbit Polyclonal anti-S100A8 Proteintech Cat# 15792-1-AP; RRID: AB_10666315
Rabbit Monoclonal anti-αSMA Abcam Cat# ab124964; RRID: AB_11129103
Rabbit Monoclonal anti-Collagen 1A1 Cell Signaling Technology Cat# 72026; RRID: AB_2904565
Rabbit Monoclonal anti-FAK Abcam Cat# ab40794; RRID: AB_732300
Rabbit Monoclonal anti-phospho-FAK (Tyr 397) Cell Signaling Technology Cat# 8556; RRID: AB_10891442
Rabbit Monoclonal anti-Src Cell Signaling Technology Cat# 2123; RRID: AB_2106047
Rabbit Monoclonal anti-phospho-Src (Tyr 416) Cell Signaling Technology Cat# 6943; RRID: AB_10013641
Rabbit Polyclonal anti-CD31 Servicebio Cat# GB11063-2-100; RRID: AB_2922436
Rabbit Polyclonal anti-CXCL1 Proteintech Cat# 12335-1-AP; RRID: AB_2087568
Mouse Monoclonal anti-RhoA-GTP NewEast Biosciences Cat# 26904; RRID: AB_1961799
Rabbit Monoclonal anti-RhoA Cell Signaling Technology Cat# 2117; RRID: AB_10693922
Rabbit Monoclonal anti-ROCK1 Cell Signaling Technology Cat# 4035; RRID: AB_2238679
Rabbit Monoclonal anti-phospho-MLC2 (Ser 19) Cell Signaling Technology Cat# 3671; RRID: AB_330248
Rabbit Monoclonal anti-MLC2 Cell Signaling Technology Cat# 8505; RRID: AB_2728760
Rabbit Polyclonal anti-MRTF-A Proteintech Cat# 21166-1-AP; RRID: AB_2878822
Rabbit Polyclonal anti-CD147 Proteintech Cat# 11989-1-AP; RRID: AB_2290597
Rabbit Monoclonal anti-phospho-ERK1/2 (Thr 202/Tyr 204) Cell Signaling Technology Cat# 4370; RRID: AB_2315112
Rabbit Monoclonal anti-ERK1/2 Cell Signaling Technology Cat# 4695; RRID: AB_390779
Rabbit Monoclonal anti-cleaved-PARP (Asp 214) Cell Signaling Technology Cat# 5625; RRID: AB_10699459
Rabbit Monoclonal anti-cleaved-Caspase3 (Asp 175) Cell Signaling Technology Cat# 9661; RRID: AB_2341188
Rabbit Polyclonal anti-TFAP2A Proteintech Cat# 13019-3-AP; RRID: AB_2199414
Mouse Monoclonal anti-Vinculin Proteintech Cat# 66305-1-Ig; RRID: AB_2810300
Mouse Monoclonal anti-GAPDH Proteintech Cat# 60004-1-Ig; RRID: AB_2107436
Normal Rabbit IgG Cell Signaling Technology Cat# 2729; RRID: AB_1031062
Rabbit monoclonal anti-Histone H3 Cell Signaling Technology Cat# 4620; RRID: AB_1904005
Goat anti-rabbit IgG, HRP-linked Cell Signaling Technology Cat# 7074; RRID: AB_2099233
Horse anti-mouse IgG, HRP-linked Cell Signaling Technology Cat# 7076; RRID: AB_330924

Bacterial and virus strains

S100A8 shRNA lentivirus Genechem N/A
S100A8 overexpression lentivirus Genechem N/A
CD147 Cas9-sgRNA lentivirus Genechem N/A

Biological samples

ESCC tumor specimens Linzhou Cancer Hospital See Table S1 for details

Chemicals, peptides, and recombinant proteins

DMEM Corning Cat# 10-013-CV
Advanced DMEM/F12 Gibco Cat# 12634028
Fetal Bovine Serum Cell Technologies Cat# 30070
5-Fluorouracil MCE Cat# HY-90006
Cisplatin MCE Cat# HY-17394
Collagenase I Gibco Cat# 17100017
Collagenase IV Gibco Cat# 17104019
Hyaluronidase Sigma-Aldrich Cat# H1115000
B-27 Gibco Cat# 17504044
HEPES Gibco Cat# 15630080
GlutaMAX™ Gibco Cat# 35050061
EGF Gibco Cat# PMG8043
Y-27632 Selleck Chemicals Cat# S1049
A83-01 Tocris Bioscience Cat# 2939
Puromycin Gibco Cat# A1113803
Lipofectamine 2000 Invitrogen Cat# 11668027
AC-73 MCE Cat# HY-122214
Human recombinant S100A8 protein Novoprotein Cat# C794
Triton X-100 Solarbio Cat# T8200

Critical commercial assays

RNA-Quick Purification Kit ES Science Cat# RN001
TB Green® Premix Ex Taq™II (Tli RNaseH Plus) TaKaRa Cat# RR820A
Masson’s Trichrome Stain Kit Solarbio Cat# G1340
Meilunbio® FGSuper Sensitive ECL Luminescence Reagent Meilunbio Cat# MA0186-1
Pierce™ Rapid Gold BCA Thermo Fisher Scientific Cat# A53226
Human S100A8/S100A9 ELISA Kit Proteintech Cat# KE00177
Opal 5-Color Manual IHC Kit PANOVUE Cat# 10144100100
SimpleChIP® Plus Sonication Chromatin IP Kit Cell Signaling Technology Cat# 56383

Deposited data

RNA-seq data of PDX mice This paper GSA: CRA013775
RNA-seq data of PDX donors Yang et al.25 GSA: HRA004329
ESCC scRNA-seq data Zhang et al.20 GEO: GSE160269

Experimental models: Cell lines

KYSE450 Dr. Y. Shimada JCRB1430
KYSE510 Dr. Y. Shimada JCRB1436
KYSE180 Dr. Y. Shimada JCRB1083
Human esophageal cancer associated fibroblasts (ECAFs) This paper N/A
PDX-derived primary tumor cells (PDCs) This paper N/A

Experimental models: Organisms/strains

NSG mouse BEIJING IDMO Co., Ltd N/A

Oligonucleotides

shRNA sequences, see Table S2 Genechem N/A
sgRNA sequences, see Table S2 Genechem N/A
siRNA, see Table S2 JTSBIO Co.,Ltd (Wuhan, China) N/A
qRT-PCR primers, see Table S3 Tsingke Biotechnology N/A

Software and algorithms

R 4.2.2 R Core Team https://www.R-project.org/
Trim Galore (version 0.6.6) Felix Krueger https://github.com/FelixKrueger/TrimGalore
Disambiguate (version 1.0) Ahdesmäki et al.35 https://github.com/AstraZeneca-NGS/disambiguate
Salmon (version 1.2.0) Patro et al.84 https://combine-lab.github.io/salmon/
DESeq2 (version 1.38.3) Love et al.85 https://bioconductor.org/packages/DESeq2/
tximport (version 1.26.1) Soneson et al.86 https://bioconductor.org/packages/tximport/
clusterProfiler (version 4.6.2) Wu et al.87 https://github.com/YuLab-SMU/clusterProfiler
Seurat (version 4.3.0) Hao et al.88 https://github.com/satijalab/seurat
Harmony (version 0.1.1) Korsunsky et al.89 https://github.com/immunogenomics/harmony
CellChat (version 1.6.1) Jin et al.90 https://github.com/sqjin/CellChat
survminer (version 0.4.9) Kassambara et al. https://github.com/kassambara/survminer
ImageJ NIH https://imagej.nih.gov/ij/
Prism 8.0 GraphPad http://www.graphpad.com/