ZMAT5 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-67dox	BGRSDLV02-68dox
idx	0	0
TRCN#_or_BGC#	TRCN0000155138	TRCN0000155138
shRNA_or_gRNA_sequence	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG	CCGGGAAGGTCTGGTACGACATGTTCTCGAGAACATGTCGTACCAGACCTTCTTTTTTG
PAM
Name	ZMAT5	ZMAT5
Sample_ID	BGRSDLV02-67dox	BGRSDLV02-68dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZMAT5	ZMAT5
qPCR_result	89.4	88.6
Ave_qPCR	89.0
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9278	9279

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-67dox	BGRSDLV02-68dox
Sample_ID	BGRSDLV02-67dox	BGRSDLV02-68dox
Sample Name
Sample Name	ZMAT5-BGRSDLV02-67dox	ZMAT5-BGRSDLV02-68dox
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	12378	12379

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-67dox	BGRSDLV02-68dox
Sample #	59	60
Sample Name	ZMAT5-BGRSDLV02-67dox	ZMAT5-BGRSDLV02-68dox
Sample_Name_Alias
Index Well Position	C08	D08
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	292	295
Peak_Molarity	76.80	76.80
libSampleQC_DNA_Well	DNA_Library_set65/set1/C8.png	DNA_Library_set65/set1/D8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C8.png	RNA_Library_set65/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-67dox	BGRSDLV02-68dox
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	3980	3981

Sequencing Information

	BGRSDLV02-67dox	BGRSDLV02-68dox
Sample_ID	BGRSDLV02-67dox	BGRSDLV02-68dox
Sample Name	ZMAT5-BGRSDLV02-67dox	ZMAT5-BGRSDLV02-68dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	29,878,919	20,749,058
total_aligned_reads	26,804,274	19,596,906
unique_aligned_reads	24,989,937	18,249,928
percent_uniqueAligned	0.83637	0.87955
correlation_replicates	0.988782	0.988782
spikein_reads	4,852	2,936
percent_spikeins	0.00016	0.00014
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2727	2728

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-BGRSDLV02-67dox_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2727	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8800
ZMAT5-BGRSDLV02-67dox_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2727	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8876
ZMAT5-BGRSDLV02-67dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-67dox_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9365
ZMAT5-BGRSDLV02-67dox_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	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	9441
ZMAT5-BGRSDLV02-67dox_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	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	9517
ZMAT5-BGRSDLV02-67dox_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	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	9593
ZMAT5-BGRSDLV02-67dox_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	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox/Aligned.sortedByCoord.out.bam		ENCORE2	9669
ZMAT5-BGRSDLV02-67dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2727					GRCh38	V40	ZMAT5-BGRSDLV02-67dox_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-67dox_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9745
ZMAT5-BGRSDLV02-68dox_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2728	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8801
ZMAT5-BGRSDLV02-68dox_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2728	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8877
ZMAT5-BGRSDLV02-68dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-68dox_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9366
ZMAT5-BGRSDLV02-68dox_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	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	9442
ZMAT5-BGRSDLV02-68dox_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	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	9518
ZMAT5-BGRSDLV02-68dox_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	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	9594
ZMAT5-BGRSDLV02-68dox_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	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox/Aligned.sortedByCoord.out.bam		ENCORE2	9670
ZMAT5-BGRSDLV02-68dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2728					GRCh38	V40	ZMAT5-BGRSDLV02-68dox_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT5-BGRSDLV02-68dox_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9746