ZMAT3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-63dox	BGRSDLV02-64dox
idx	0	0
TRCN#_or_BGC#	TRCN0000128165	TRCN0000128165
shRNA_or_gRNA_sequence	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG
PAM
Name	ZMAT3	ZMAT3
Sample_ID	BGRSDLV02-63dox	BGRSDLV02-64dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	ZMAT3	ZMAT3
qPCR_result	86.0	83.4
Ave_qPCR	84.7
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	9274	9275

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-63dox	BGRSDLV02-64dox
Sample_ID	BGRSDLV02-63dox	BGRSDLV02-64dox
Sample Name
Sample Name	ZMAT3-BGRSDLV02-63dox	ZMAT3-BGRSDLV02-64dox
RBP	ZMAT3	ZMAT3
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12374	12375

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-63dox	BGRSDLV02-64dox
Sample #	55	56
Sample Name	ZMAT3-BGRSDLV02-63dox	ZMAT3-BGRSDLV02-64dox
Sample_Name_Alias
Index Well Position	G07	H07
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	290
Peak_Molarity	77.80	74.60
libSampleQC_DNA_Well	DNA_Library_set65/set1/G7.png	DNA_Library_set65/set1/H7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set65/set1/G7.png	RNA_Library_set65/set1/H7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-63dox	BGRSDLV02-64dox
RBP	ZMAT3	ZMAT3
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	3976	3977

Sequencing Information

	BGRSDLV02-63dox	BGRSDLV02-64dox
Sample_ID	BGRSDLV02-63dox	BGRSDLV02-64dox
Sample Name	ZMAT3-BGRSDLV02-63dox	ZMAT3-BGRSDLV02-64dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	31,708,273	31,512,420
total_aligned_reads	29,387,375	29,557,157
unique_aligned_reads	27,413,879	27,678,336
percent_uniqueAligned	0.86457	0.87833
correlation_replicates	0.996156	0.996156
spikein_reads	2,844	9,272
percent_spikeins	0.00009	0.00029
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2723	2724

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-BGRSDLV02-63dox_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2723	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	8796
ZMAT3-BGRSDLV02-63dox_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2723	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	8872
ZMAT3-BGRSDLV02-63dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSDLV02-63dox_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9361
ZMAT3-BGRSDLV02-63dox_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	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox/Aligned.sortedByCoord.out.bam		ENCORE2	9437
ZMAT3-BGRSDLV02-63dox_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	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox/Aligned.sortedByCoord.out.bam		ENCORE2	9513
ZMAT3-BGRSDLV02-63dox_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	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox/Aligned.sortedByCoord.out.bam		ENCORE2	9589
ZMAT3-BGRSDLV02-63dox_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	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox/Aligned.sortedByCoord.out.bam		ENCORE2	9665
ZMAT3-BGRSDLV02-63dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2723					GRCh38	V40	ZMAT3-BGRSDLV02-63dox_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSDLV02-63dox_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9741
ZMAT3-BGRSDLV02-64dox_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2724	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	8797
ZMAT3-BGRSDLV02-64dox_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2724	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	8873
ZMAT3-BGRSDLV02-64dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSDLV02-64dox_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9362
ZMAT3-BGRSDLV02-64dox_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	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox/Aligned.sortedByCoord.out.bam		ENCORE2	9438
ZMAT3-BGRSDLV02-64dox_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	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox/Aligned.sortedByCoord.out.bam		ENCORE2	9514
ZMAT3-BGRSDLV02-64dox_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	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox/Aligned.sortedByCoord.out.bam		ENCORE2	9590
ZMAT3-BGRSDLV02-64dox_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	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox/Aligned.sortedByCoord.out.bam		ENCORE2	9666
ZMAT3-BGRSDLV02-64dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2724					GRCh38	V40	ZMAT3-BGRSDLV02-64dox_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSDLV02-64dox_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9742