ZMAT3 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-53	BG293LV05-54
idx	0	0
TRCN#_or_BGC#	TRCN0000128165	TRCN0000128165
shRNA_or_gRNA_sequence	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG
PAM
Name	ZMAT3	ZMAT3
Sample_ID	BG293LV05-53	BG293LV05-54
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	ZMAT3	ZMAT3
qPCR_result	88.2	91.1
Ave_qPCR	89.65
RT-qPCR_primer-F	gggaagaatcatgccaagag
RT-qPCR_primer-R	ttgacccagctctgaggatt
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	10025	10026

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-53	BG293LV05-54
Sample_ID	BG293LV05-53	BG293LV05-54
Sample Name
Sample Name	ZMAT3-BG293LV05-53	ZMAT3-BG293LV05-54
RBP	ZMAT3	ZMAT3
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12860	12861

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-53	BG293LV05-54
Sample #	27	28
Sample Name	ZMAT3-BG293LV05-53	ZMAT3-BG293LV05-54
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	268	277
Peak_Molarity	93.70	80.10
libSampleQC_DNA_Well	DNA_Library_set69/set1/C4.png	DNA_Library_set69/set1/D4.png
RIN	9.2	9.8
libSample_RNA_Well	RNA_Library_set69/set1/D9.png	RNA_Library_set69/set1/E9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-53	BG293LV05-54
RBP	ZMAT3	ZMAT3
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4208	4209

Sequencing Information

	BG293LV05-53	BG293LV05-54
Sample_ID	BG293LV05-53	BG293LV05-54
Sample Name	ZMAT3-BG293LV05-53	ZMAT3-BG293LV05-54
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	19,207,625	17,542,867
total_aligned_reads	16,367,062	14,794,529
unique_aligned_reads	15,267,222	13,860,469
percent_uniqueAligned	0.79485	0.79009
correlation_replicates	0.987325	0.987325
spikein_reads	5,184	1,716
percent_spikeins	0.00027	0.00010
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2927	2928

Data Submission Information DCC submission information was not avaliable

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
ZMAT3-BG293LV05-53_S159_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2927	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28535
ZMAT3-BG293LV05-53_S159_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2927	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28579
ZMAT3-BG293LV05-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53_S159_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV05-53_S159_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28623
ZMAT3-BG293LV05-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53/Aligned.sortedByCoord.out.bam		ENCORE2	28667
ZMAT3-BG293LV05-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53/Aligned.sortedByCoord.out.bam		ENCORE2	28711
ZMAT3-BG293LV05-53_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53/Aligned.sortedByCoord.out.bam		ENCORE2	28755
ZMAT3-BG293LV05-53_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53/Aligned.sortedByCoord.out.bam		ENCORE2	28799
ZMAT3-BG293LV05-53_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2927					GRCh38	V40	ZMAT3-BG293LV05-53_S159_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV05-53_S159_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28843
ZMAT3-BG293LV05-54_S160_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2928	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28536
ZMAT3-BG293LV05-54_S160_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2928	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28580
ZMAT3-BG293LV05-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54_S160_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV05-54_S160_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28624
ZMAT3-BG293LV05-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54/Aligned.sortedByCoord.out.bam		ENCORE2	28668
ZMAT3-BG293LV05-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54/Aligned.sortedByCoord.out.bam		ENCORE2	28712
ZMAT3-BG293LV05-54_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54/Aligned.sortedByCoord.out.bam		ENCORE2	28756
ZMAT3-BG293LV05-54_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54/Aligned.sortedByCoord.out.bam		ENCORE2	28800
ZMAT3-BG293LV05-54_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2928					GRCh38	V40	ZMAT3-BG293LV05-54_S160_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV05-54_S160_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28844