MBNL2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-5	BGRSLV06-6
idx	0	0
TRCN#_or_BGC#	TRCN0000149998	TRCN0000149998
shRNA_or_gRNA_sequence	CCGGCCAGCAGATGCAATTTATGTTCTCGAGAACATAAATTGCATCTGCTGGTTTTTTG	CCGGCCAGCAGATGCAATTTATGTTCTCGAGAACATAAATTGCATCTGCTGGTTTTTTG
PAM
Name	MBNL2	MBNL2
Sample_ID	BGRSLV06-5	BGRSLV06-6
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	MBNL2	MBNL2
qPCR_result	81.7	84.9
Ave_qPCR	83.3
RT-qPCR_primer-F	cttcatccagtgcccacttt
RT-qPCR_primer-R	caggggttacaggtgctagg
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	8532	8533

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-5	BGRSLV06-6
Sample_ID	BGRSLV06-5	BGRSLV06-6
Sample Name
Sample Name	MBNL2-BGRSLV06-5	MBNL2-BGRSLV06-6
RBP	MBNL2	MBNL2
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11686	11687

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-5	BGRSLV06-6
Sample #	69	70
Sample Name	MBNL2-BGRSLV06-5	MBNL2-BGRSLV06-6
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	286	289
Peak_Molarity	102.00	110.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A10.png	DNA_Library_set60-62/set1/B10.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set60-62/set1/E9.png	RNA_Library_set60-62/set1/F9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-5	BGRSLV06-6
RBP	MBNL2	MBNL2
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3656	3657

Sequencing Information

	BGRSLV06-5	BGRSLV06-6
Sample_ID	BGRSLV06-5	BGRSLV06-6
Sample Name	MBNL2-BGRSLV06-5	MBNL2-BGRSLV06-6
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	29,844,725	26,913,644
total_aligned_reads	26,637,513	22,627,104
unique_aligned_reads	25,043,955	21,249,118
percent_uniqueAligned	0.83914	0.78953
correlation_replicates	0.996186	0.996186
spikein_reads	65,460	42,718
percent_spikeins	0.00219	0.00159
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2527	2528

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
MBNL2-BGRSLV06-5_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2527	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8578
MBNL2-BGRSLV06-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,MBNL2-BGRSLV06-5_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10443
MBNL2-BGRSLV06-5_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5/Aligned.sortedByCoord.out.bam		ENCORE2	10495
MBNL2-BGRSLV06-5_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5/Aligned.sortedByCoord.out.bam		ENCORE2	10547
MBNL2-BGRSLV06-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5/Aligned.sortedByCoord.out.bam		ENCORE2	10599
MBNL2-BGRSLV06-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5/Aligned.sortedByCoord.out.bam		ENCORE2	10651
MBNL2-BGRSLV06-5_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2527					GRCh38	V40	MBNL2-BGRSLV06-5_S69_L002_R1_001.filtered.trimmed.paired.fastq.gz,MBNL2-BGRSLV06-5_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10703
MBNL2-BGRSLV06-5_S69_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2527	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28845
MBNL2-BGRSLV06-6_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2528	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8579
MBNL2-BGRSLV06-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,MBNL2-BGRSLV06-6_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10444
MBNL2-BGRSLV06-6_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6/Aligned.sortedByCoord.out.bam		ENCORE2	10496
MBNL2-BGRSLV06-6_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6/Aligned.sortedByCoord.out.bam		ENCORE2	10548
MBNL2-BGRSLV06-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6/Aligned.sortedByCoord.out.bam		ENCORE2	10600
MBNL2-BGRSLV06-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6/Aligned.sortedByCoord.out.bam		ENCORE2	10652
MBNL2-BGRSLV06-6_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2528					GRCh38	V40	MBNL2-BGRSLV06-6_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,MBNL2-BGRSLV06-6_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10704
MBNL2-BGRSLV06-6_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2528	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28846