MAZ RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-47dox	BGRSDLV02-48dox
idx	0	0
TRCN#_or_BGC#	TRCN0000235699	TRCN0000235699
shRNA_or_gRNA_sequence	CCGGGATGCTGAGCTCGGCTTATATCTCGAGATATAAGCCGAGCTCAGCATCTTTTTG	CCGGGATGCTGAGCTCGGCTTATATCTCGAGATATAAGCCGAGCTCAGCATCTTTTTG
PAM
Name	MAZ	MAZ
Sample_ID	BGRSDLV02-47dox	BGRSDLV02-48dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	MAZ	MAZ
qPCR_result	89.8	93.1
Ave_qPCR	91.4
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	9258	9259

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-47dox	BGRSDLV02-48dox
Sample_ID	BGRSDLV02-47dox	BGRSDLV02-48dox
Sample Name
Sample Name	MAZ-BGRSDLV02-47dox	MAZ-BGRSDLV02-48dox
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	12362	12363

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-47dox	BGRSDLV02-48dox
Sample #	43	44
Sample Name	MAZ-BGRSDLV02-47dox	MAZ-BGRSDLV02-48dox
Sample_Name_Alias
Index Well Position	C06	D06
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	297
Peak_Molarity	93.20	87.10
libSampleQC_DNA_Well	DNA_Library_set65/set1/C6.png	DNA_Library_set65/set1/D6.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set65/set1/C6.png	RNA_Library_set65/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-47dox	BGRSDLV02-48dox
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	3964	3965

Sequencing Information

	BGRSDLV02-47dox	BGRSDLV02-48dox
Sample_ID	BGRSDLV02-47dox	BGRSDLV02-48dox
Sample Name	MAZ-BGRSDLV02-47dox	MAZ-BGRSDLV02-48dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	24,579,917	28,194,558
total_aligned_reads	22,837,904	26,222,692
unique_aligned_reads	21,311,557	24,419,875
percent_uniqueAligned	0.86703	0.86612
correlation_replicates	0.993443	0.993443
spikein_reads	4,826	4,702
percent_spikeins	0.00020	0.00017
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2711	2712

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-BGRSDLV02-47dox_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2711	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	8780
MAZ-BGRSDLV02-47dox_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2711	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	8856
MAZ-BGRSDLV02-47dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-47dox_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9345
MAZ-BGRSDLV02-47dox_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	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9421
MAZ-BGRSDLV02-47dox_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	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9497
MAZ-BGRSDLV02-47dox_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	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9573
MAZ-BGRSDLV02-47dox_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	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9649
MAZ-BGRSDLV02-47dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2711					GRCh38	V40	MAZ-BGRSDLV02-47dox_S43_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-47dox_S43_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9725
MAZ-BGRSDLV02-48dox_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2712	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	8781
MAZ-BGRSDLV02-48dox_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2712	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	8857
MAZ-BGRSDLV02-48dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-48dox_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9346
MAZ-BGRSDLV02-48dox_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	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9422
MAZ-BGRSDLV02-48dox_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	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9498
MAZ-BGRSDLV02-48dox_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	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9574
MAZ-BGRSDLV02-48dox_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	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9650
MAZ-BGRSDLV02-48dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2712					GRCh38	V40	MAZ-BGRSDLV02-48dox_S44_L001_R1_001.filtered.trimmed.paired.fastq.gz,MAZ-BGRSDLV02-48dox_S44_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9726