MAZ RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-45	BGRSDLV02-46
idx	0	0
TRCN#_or_BGC#	TRCN0000235699	TRCN0000235699
shRNA_or_gRNA_sequence	CCGGGATGCTGAGCTCGGCTTATATCTCGAGATATAAGCCGAGCTCAGCATCTTTTTG	CCGGGATGCTGAGCTCGGCTTATATCTCGAGATATAAGCCGAGCTCAGCATCTTTTTG
PAM
Name	MAZ	MAZ
Sample_ID	BGRSDLV02-45	BGRSDLV02-46
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	MAZ	MAZ
qPCR_result	89.0	92.6
Ave_qPCR	90.8
RT-qPCR_primer-F	gaccacatgaaggtgcacag
RT-qPCR_primer-R	gtatgctgccgtggtgaag
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	9256	9257

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-45	BGRSDLV02-46
Sample_ID	BGRSDLV02-45	BGRSDLV02-46
Sample Name
Sample Name	MAZ-BGRSDLV02-45	MAZ-BGRSDLV02-46
RBP	MAZ	MAZ
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12360	12361

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-45	BGRSDLV02-46
Sample #	41	42
Sample Name	MAZ-BGRSDLV02-45	MAZ-BGRSDLV02-46
Sample_Name_Alias
Index Well Position	A06	B06
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	287	296
Peak_Molarity	69.60	81.60
libSampleQC_DNA_Well	DNA_Library_set65/set1/A6.png	DNA_Library_set65/set1/B6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set65/set1/A6.png	RNA_Library_set65/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-45	BGRSDLV02-46
RBP	MAZ	MAZ
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	3962	3963

Sequencing Information

	BGRSDLV02-45	BGRSDLV02-46
Sample_ID	BGRSDLV02-45	BGRSDLV02-46
Sample Name	MAZ-BGRSDLV02-45	MAZ-BGRSDLV02-46
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	38,833,103	30,148,654
total_aligned_reads	36,334,941	27,942,502
unique_aligned_reads	33,941,647	26,078,728
percent_uniqueAligned	0.87404	0.86500
correlation_replicates	0.995103	0.995103
spikein_reads	14,468	6,054
percent_spikeins	0.00037	0.00020
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2709	2710

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
MAZ-BGRSDLV02-45_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2709	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	8778
MAZ-BGRSDLV02-45_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2709	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	8854
MAZ-BGRSDLV02-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2709					GRCh38	V40	MAZ-BGRSDLV02-45_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-45_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9343
MAZ-BGRSDLV02-45_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	2709					GRCh38	V40	MAZ-BGRSDLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	9419
MAZ-BGRSDLV02-45_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	2709					GRCh38	V40	MAZ-BGRSDLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	9495
MAZ-BGRSDLV02-45_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	2709					GRCh38	V40	MAZ-BGRSDLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	9571
MAZ-BGRSDLV02-45_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	2709					GRCh38	V40	MAZ-BGRSDLV02-45/Aligned.sortedByCoord.out.bam		ENCORE2	9647
MAZ-BGRSDLV02-45_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2709					GRCh38	V40	MAZ-BGRSDLV02-45_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-45_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9723
MAZ-BGRSDLV02-46_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2710	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	8779
MAZ-BGRSDLV02-46_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2710	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	8855
MAZ-BGRSDLV02-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2710					GRCh38	V40	MAZ-BGRSDLV02-46_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-46_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9344
MAZ-BGRSDLV02-46_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	2710					GRCh38	V40	MAZ-BGRSDLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	9420
MAZ-BGRSDLV02-46_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	2710					GRCh38	V40	MAZ-BGRSDLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	9496
MAZ-BGRSDLV02-46_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	2710					GRCh38	V40	MAZ-BGRSDLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	9572
MAZ-BGRSDLV02-46_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	2710					GRCh38	V40	MAZ-BGRSDLV02-46/Aligned.sortedByCoord.out.bam		ENCORE2	9648
MAZ-BGRSDLV02-46_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2710					GRCh38	V40	MAZ-BGRSDLV02-46_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-46_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9724