MBNL1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-27dox	BGRSDLV03-28dox
idx	0	0
TRCN#_or_BGC#	TRCN0000063964	TRCN0000063964
shRNA_or_gRNA_sequence	CCGGGCCAACCAGATACCCATAATACTCGAGTATTATGGGTATCTGGTTGGCTTTTTG	CCGGGCCAACCAGATACCCATAATACTCGAGTATTATGGGTATCTGGTTGGCTTTTTG
PAM
Name	MBNL1	MBNL1
Sample_ID	BGRSDLV03-27dox	BGRSDLV03-28dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	MBNL1	MBNL1
qPCR_result	48.5	48.1
Ave_qPCR	48.3
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	9341	9342

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-27dox	BGRSDLV03-28dox
Sample_ID	BGRSDLV03-27dox	BGRSDLV03-28dox
Sample Name
Sample Name	MBNL1-BGRSDLV03-27dox	MBNL1-BGRSDLV03-28dox
RBP	MBNL1	MBNL1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12620	12621

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-27dox	BGRSDLV03-28dox
Sample #	23	24
Sample Name	MBNL1-BGRSDLV03-27dox	MBNL1-BGRSDLV03-28dox
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	277	269
Peak_Molarity	48.60	58.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/G8.png	DNA_Library_set66/set1/H8.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set66/set1/G3.png	RNA_Library_set66/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-27dox	BGRSDLV03-28dox
RBP	MBNL1	MBNL1
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4056	4057

Sequencing Information

	BGRSDLV03-27dox	BGRSDLV03-28dox
Sample_ID	BGRSDLV03-27dox	BGRSDLV03-28dox
Sample Name	MBNL1-BGRSDLV03-27dox	MBNL1-BGRSDLV03-28dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,757,144	12,379,228
total_aligned_reads	12,092,028	10,964,921
unique_aligned_reads	11,247,786	10,185,769
percent_uniqueAligned	0.81760	0.82281
correlation_replicates	0.997956	0.997956
spikein_reads	3,478	3,248
percent_spikeins	0.00025	0.00026
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2775	2776

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
MBNL1-BGRSDLV03-27dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2775	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8924
MBNL1-BGRSDLV03-27dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2775	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8964
MBNL1-BGRSDLV03-27dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-27dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9004
MBNL1-BGRSDLV03-27dox_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9044
MBNL1-BGRSDLV03-27dox_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9084
MBNL1-BGRSDLV03-27dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9124
MBNL1-BGRSDLV03-27dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox/Aligned.sortedByCoord.out.bam		ENCORE2	9164
MBNL1-BGRSDLV03-27dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2775					GRCh38	V40	MBNL1-BGRSDLV03-27dox_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-27dox_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9204
MBNL1-BGRSDLV03-28dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2776	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8925
MBNL1-BGRSDLV03-28dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2776	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8965
MBNL1-BGRSDLV03-28dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-28dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9005
MBNL1-BGRSDLV03-28dox_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9045
MBNL1-BGRSDLV03-28dox_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9085
MBNL1-BGRSDLV03-28dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9125
MBNL1-BGRSDLV03-28dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox/Aligned.sortedByCoord.out.bam		ENCORE2	9165
MBNL1-BGRSDLV03-28dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2776					GRCh38	V40	MBNL1-BGRSDLV03-28dox_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-28dox_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9205