ZMAT5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-55	BGRSLV03-56
idx	0	0
TRCN#_or_BGC#	TRCN0000155138	TRCN0000155138
shRNA_or_gRNA_sequence	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG
PAM
Name	ZMAT5	ZMAT5
Sample_ID	BGRSLV03-55	BGRSLV03-56
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZMAT5	ZMAT5
qPCR_result	91.1	94.5
Ave_qPCR	92.8
RT-qPCR_primer-F	tgctggatgagcagaacaag
RT-qPCR_primer-R	atctgcagttggagccaaag
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	8365	8366

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-55	BGRSLV03-56
Sample_ID	BGRSLV03-55	BGRSLV03-56
Sample Name
Sample Name	ZMAT5-BGRSLV03-55	ZMAT5-BGRSLV03-56
RBP	ZMAT5	ZMAT5
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11402	11403

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-55	BGRSLV03-56
Sample #	33	34
Sample Name	ZMAT5-BGRSLV03-55	ZMAT5-BGRSLV03-56
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	294	290
Peak_Molarity	55.00	84.30
libSampleQC_DNA_Well	DNA_Library_set58/set1/A11.png	DNA_Library_set58/set1/B11.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set58/set1/A5.png	RNA_Library_set58/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-55	BGRSLV03-56
RBP	ZMAT5	ZMAT5
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3540	3541

Sequencing Information

	BGRSLV03-55	BGRSLV03-56
Sample_ID	BGRSLV03-55	BGRSLV03-56
Sample Name	ZMAT5-BGRSLV03-55	ZMAT5-BGRSLV03-56
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	42,642,016	53,049,344
total_aligned_reads	32,615,323	46,886,420
unique_aligned_reads	30,519,442	43,907,258
percent_uniqueAligned	0.71571	0.82767
correlation_replicates	0.995537	0.995537
spikein_reads	279,382	403,962
percent_spikeins	0.00655	0.00761
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2411	2412

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
ZMAT5-BGRSLV03-55_S167_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2411	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8158
ZMAT5-BGRSLV03-55_S167_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2411	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8200
ZMAT5-BGRSLV03-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55_S167_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSLV03-55_S167_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11279
ZMAT5-BGRSLV03-55_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55/Aligned.sortedByCoord.out.bam		ENCORE2	11321
ZMAT5-BGRSLV03-55_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55/Aligned.sortedByCoord.out.bam		ENCORE2	11363
ZMAT5-BGRSLV03-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55/Aligned.sortedByCoord.out.bam		ENCORE2	11405
ZMAT5-BGRSLV03-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55/Aligned.sortedByCoord.out.bam		ENCORE2	11447
ZMAT5-BGRSLV03-55_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2411					GRCh38	V40	ZMAT5-BGRSLV03-55_S167_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSLV03-55_S167_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11489
ZMAT5-BGRSLV03-56_S168_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2412	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8159
ZMAT5-BGRSLV03-56_S168_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2412	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8201
ZMAT5-BGRSLV03-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56_S168_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSLV03-56_S168_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11280
ZMAT5-BGRSLV03-56_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56/Aligned.sortedByCoord.out.bam		ENCORE2	11322
ZMAT5-BGRSLV03-56_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56/Aligned.sortedByCoord.out.bam		ENCORE2	11364
ZMAT5-BGRSLV03-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56/Aligned.sortedByCoord.out.bam		ENCORE2	11406
ZMAT5-BGRSLV03-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56/Aligned.sortedByCoord.out.bam		ENCORE2	11448
ZMAT5-BGRSLV03-56_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2412					GRCh38	V40	ZMAT5-BGRSLV03-56_S168_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSLV03-56_S168_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11490