MBNL1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-25	BGRSDLV03-26
idx	0	0
TRCN#_or_BGC#	TRCN0000063964	TRCN0000063964
shRNA_or_gRNA_sequence	CCGGGCCAACCAGATACCCATAATACTCGAGTATTATGGGTATCTGGTTGGCTTTTTG	CCGGGCCAACCAGATACCCATAATACTCGAGTATTATGGGTATCTGGTTGGCTTTTTG
PAM
Name	MBNL1	MBNL1
Sample_ID	BGRSDLV03-25	BGRSDLV03-26
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	MBNL1	MBNL1
qPCR_result	51.2	56.7
Ave_qPCR	54.0
RT-qPCR_primer-F	ctgccgaacatctgactagc
RT-qPCR_primer-R	atggctaatgacctcgtcct
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	9339	9340

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-25	BGRSDLV03-26
Sample_ID	BGRSDLV03-25	BGRSDLV03-26
Sample Name
Sample Name	MBNL1-BGRSDLV03-25	MBNL1-BGRSDLV03-26
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	12618	12619

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-25	BGRSDLV03-26
Sample #	21	22
Sample Name	MBNL1-BGRSDLV03-25	MBNL1-BGRSDLV03-26
Sample_Name_Alias
Index Well Position	E07	F07
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	280	279
Peak_Molarity	50.30	55.60
libSampleQC_DNA_Well	DNA_Library_set66/set1/E8.png	DNA_Library_set66/set1/F8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set66/set1/E3.png	RNA_Library_set66/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-25	BGRSDLV03-26
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	4054	4055

Sequencing Information

	BGRSDLV03-25	BGRSDLV03-26
Sample_ID	BGRSDLV03-25	BGRSDLV03-26
Sample Name	MBNL1-BGRSDLV03-25	MBNL1-BGRSDLV03-26
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,434,889	12,569,676
total_aligned_reads	11,508,980	11,210,950
unique_aligned_reads	10,676,439	10,440,963
percent_uniqueAligned	0.79468	0.83065
correlation_replicates	0.997545	0.997545
spikein_reads	1,952	2,718
percent_spikeins	0.00015	0.00022
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2773	2774

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-BGRSDLV03-25_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2773	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8922
MBNL1-BGRSDLV03-25_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2773	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8962
MBNL1-BGRSDLV03-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2773					GRCh38	V40	MBNL1-BGRSDLV03-25_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-25_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9002
MBNL1-BGRSDLV03-25_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	2773					GRCh38	V40	MBNL1-BGRSDLV03-25/Aligned.sortedByCoord.out.bam		ENCORE2	9042
MBNL1-BGRSDLV03-25_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	2773					GRCh38	V40	MBNL1-BGRSDLV03-25/Aligned.sortedByCoord.out.bam		ENCORE2	9082
MBNL1-BGRSDLV03-25_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	2773					GRCh38	V40	MBNL1-BGRSDLV03-25/Aligned.sortedByCoord.out.bam		ENCORE2	9122
MBNL1-BGRSDLV03-25_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	2773					GRCh38	V40	MBNL1-BGRSDLV03-25/Aligned.sortedByCoord.out.bam		ENCORE2	9162
MBNL1-BGRSDLV03-25_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2773					GRCh38	V40	MBNL1-BGRSDLV03-25_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-25_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9202
MBNL1-BGRSDLV03-26_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2774	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8923
MBNL1-BGRSDLV03-26_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2774	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8963
MBNL1-BGRSDLV03-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2774					GRCh38	V40	MBNL1-BGRSDLV03-26_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-26_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9003
MBNL1-BGRSDLV03-26_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	2774					GRCh38	V40	MBNL1-BGRSDLV03-26/Aligned.sortedByCoord.out.bam		ENCORE2	9043
MBNL1-BGRSDLV03-26_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	2774					GRCh38	V40	MBNL1-BGRSDLV03-26/Aligned.sortedByCoord.out.bam		ENCORE2	9083
MBNL1-BGRSDLV03-26_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	2774					GRCh38	V40	MBNL1-BGRSDLV03-26/Aligned.sortedByCoord.out.bam		ENCORE2	9123
MBNL1-BGRSDLV03-26_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	2774					GRCh38	V40	MBNL1-BGRSDLV03-26/Aligned.sortedByCoord.out.bam		ENCORE2	9163
MBNL1-BGRSDLV03-26_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2774					GRCh38	V40	MBNL1-BGRSDLV03-26_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,MBNL1-BGRSDLV03-26_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9203