ZMAT5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-65	BGRSDLV02-66
idx	0	0
TRCN#_or_BGC#	TRCN0000155138	TRCN0000155138
shRNA_or_gRNA_sequence	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG
PAM
Name	ZMAT5	ZMAT5
Sample_ID	BGRSDLV02-65	BGRSDLV02-66
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZMAT5	ZMAT5
qPCR_result	91.3	88.8
Ave_qPCR	90.1
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	9276	9277

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-65	BGRSDLV02-66
Sample_ID	BGRSDLV02-65	BGRSDLV02-66
Sample Name
Sample Name	ZMAT5-BGRSDLV02-65	ZMAT5-BGRSDLV02-66
RBP	ZMAT5	ZMAT5
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12376	12377

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-65	BGRSDLV02-66
Sample #	57	58
Sample Name	ZMAT5-BGRSDLV02-65	ZMAT5-BGRSDLV02-66
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	295	305
Peak_Molarity	85.60	70.60
libSampleQC_DNA_Well	DNA_Library_set65/set1/A8.png	DNA_Library_set65/set1/B8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/A8.png	RNA_Library_set65/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-65	BGRSDLV02-66
RBP	ZMAT5	ZMAT5
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3978	3979

Sequencing Information

	BGRSDLV02-65	BGRSDLV02-66
Sample_ID	BGRSDLV02-65	BGRSDLV02-66
Sample Name	ZMAT5-BGRSDLV02-65	ZMAT5-BGRSDLV02-66
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	34,039,762	28,581,617
total_aligned_reads	31,925,009	26,952,022
unique_aligned_reads	29,791,839	25,231,673
percent_uniqueAligned	0.87521	0.88279
correlation_replicates	0.935976	0.935976
spikein_reads	11,528	4,728
percent_spikeins	0.00034	0.00017
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2725	2726

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-BGRSDLV02-65_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2725	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8798
ZMAT5-BGRSDLV02-65_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2725	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8874
ZMAT5-BGRSDLV02-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-65_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9363
ZMAT5-BGRSDLV02-65_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	9439
ZMAT5-BGRSDLV02-65_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	9515
ZMAT5-BGRSDLV02-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	9591
ZMAT5-BGRSDLV02-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	9667
ZMAT5-BGRSDLV02-65_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2725					GRCh38	V40	ZMAT5-BGRSDLV02-65_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-65_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9743
ZMAT5-BGRSDLV02-66_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2726	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8799
ZMAT5-BGRSDLV02-66_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2726	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8875
ZMAT5-BGRSDLV02-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-66_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9364
ZMAT5-BGRSDLV02-66_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	9440
ZMAT5-BGRSDLV02-66_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	9516
ZMAT5-BGRSDLV02-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	9592
ZMAT5-BGRSDLV02-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	9668
ZMAT5-BGRSDLV02-66_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2726					GRCh38	V40	ZMAT5-BGRSDLV02-66_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-66_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9744