Galectin 3: a novel biomarker of glycogen storage disease type III.

Lucille Rossiaud, Quentin Miagoux, Manon Benabidès, Océane Reiss, Louisa Jauze, Margot Jarrige Hélène Polvèche, Edoardo Malfatti, Pascal Laforêt, Giuseppe Ronzitti, Xavier Nissan, Lucile Hoch.

Description

• Team : Pharmacologie des dystrophies musculaires
• Sequencing type : Quantseq
• Samples : 21
• Organism : Human GRCh37.87
• GEO omnibus GSE272786

Tools

• FastQC ( v0.11.9 )
• cutadapt ( 4.1 )
• PRINSEQ-lite ( 0.20.4 )
• STAR ( 2.7.6a )
• samtools ( 1.13 )
• HTSeq-count ( 1.99.2 )
• R Packages ( 4.1.2 ) ( RColorBrewer, gplots, DESeq2, pheatmap , tidyverse, gridExtra, reshape, ggforce, cowplot, reshape2, viridis) ( clusterProfiler, enrichplot, org.Hs.eg.db, ggnewscale, pathview, DOSE, plyr, R.utils)

Details samples

• Size : 76 bp
• Encoding : Sanger / Illumina 1.9
• Date : 01/03/2022

Names	#Reads	#Reads post-filters	STAR : % mapped reads	# mapped reads	# Filtered mapped reads	STAR : % Filtered mapped reads
MyoT_starv2D_WT_PCi1426_B2	19 037 718	18 739 410	97,74	18 606 686	11 960 119	62,82
MyoT_starv2D_WT_PCi1426_B3	20 685 887	20 150 636	96,49	19 958 820	10 303 221	49,81
MyoT_starv2D_WT_PCi1426_B4	19 649 172	19 229 002	96,99	19 057 821	9 758 237	49,66
MyoT_starv2D_WT_i90_B1	13 839 354	13 594 602	97,57	13 503 131	7 570 791	54,70
MyoT_starv2D_WT_i90_B3	20 926 037	20 546 139	96,84	20 264 054	10 460 614	49,99
MyoT_starv2D_WT_i90_B4	18 124 459	17 672 598	96,68	17 523 180	8 049 908	44,41
MyoT_starv2D_WT_iCas9_B1	18 643 894	18 245 146	96,89	18 064 432	9 971 946	53,49
MyoT_starv2D_WT_iCas9_B2	19 568 711	18 975 160	95,47	18 682 222	10 373 533	53,01
MyoT_starv2D_WT_iCas9_B3	17 904 744	17 471 592	96,35	17 250 421	10 662 038	59,55
MyoT_starv2D_GSDIII_0576c12_B1	18 098 984	17 788 945	97,46	17 639 370	10 445 084	57,71
MyoT_starv2D_GSDIII_0576c12_B2	17 216 572	16 951 254	97,52	16 789 342	10 137 569	58,88
MyoT_starv2D_GSDIII_0576c12_B3	19 492 542	19 205 297	97,45	18 995 864	11 358 042	58,27
MyoT_starv2D_GSDIII_3390c15_B1	20 838 302	20 593 953	98,13	20 449 068	13 509 946	64,83
MyoT_starv2D_GSDIII_3390c15_B2	19 506 588	19 213 283	97,70	19 057 839	12 165 331	62,37
MyoT_starv2D_GSDIII_3390c15_B4	19 949 287	19 708 899	98,15	19 580 354	12 002 370	60,16
MyoT_starv2D_GSDIII_0303c3_B1	21 259 436	20 991 268	97,97	20 827 905	12 039 543	56,63
MyoT_starv2D_GSDIII_0303c3_B3	19 299 978	18 978 957	97,56	18 829 832	9 796 632	50,76
MyoT_starv2D_GSDIII_0303c3_B4	21 210 397	20 916 959	97,91	20 768 008	11 399 817	53,75
MyoT_starv2D_GSDIII_2523c3_B1	20 946 365	20 678 390	98,06	20 541 022	11 100 370	52,99
MyoT_starv2D_GSDIII_2523c3_B2	21 056 505	20 771 638	97,74	20 580 864	11 293 400	53,63
MyoT_starv2D_GSDIII_2523c3_B3	20 426 475	20 154 835	97,79	19 974 088	11 749 369	57,52