IGHMBP2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSDLV02-39dox	BGRSDLV02-40dox
idx	0	0
TRCN#_or_BGC#	TRCN0000019160	TRCN0000019160
shRNA_or_gRNA_sequence	CCGGCCTTTGAGTATCTTGACGATACTCGAGTATCGTCAAGATACTCAAAGGTTTTT	CCGGCCTTTGAGTATCTTGACGATACTCGAGTATCGTCAAGATACTCAAAGGTTTTT
PAM
Name	IGHMBP2	IGHMBP2
Sample_ID	BGRSDLV02-39dox	BGRSDLV02-40dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	IGHMBP2	IGHMBP2
qPCR_result	87.2	88.5
Ave_qPCR	87.8
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	11298	11299

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-39dox	BGRSDLV02-40dox
Sample_ID	BGRSDLV02-39dox	BGRSDLV02-40dox
Sample Name
Sample Name	IGHMBP2-BGRSDLV02-39dox	IGHMBP2-BGRSDLV02-40dox
RBP	IGHMBP2	IGHMBP2
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Released	Released
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	12354	12355

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-39dox	BGRSDLV02-40dox
Sample #	35	36
Sample Name	IGHMBP2-BGRSDLV02-39dox	IGHMBP2-BGRSDLV02-40dox
Sample_Name_Alias
Index Well Position	C05	D05
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	297	306
Peak_Molarity	86.20	91.40
libSampleQC_DNA_Well	DNA_Library_set65/set1/C5.png	DNA_Library_set65/set1/D5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C5.png	RNA_Library_set65/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-39dox	BGRSDLV02-40dox
RBP	IGHMBP2	IGHMBP2
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	3956	3957

Sequencing Information

	BGRSDLV02-39dox	BGRSDLV02-40dox
Sample_ID	BGRSDLV02-39dox	BGRSDLV02-40dox
Sample Name	IGHMBP2-BGRSDLV02-39dox	IGHMBP2-BGRSDLV02-40dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	42,923,632	45,648,873
total_aligned_reads	39,287,362	42,273,713
unique_aligned_reads	36,816,836	39,507,432
percent_uniqueAligned	0.85773	0.86546
correlation_replicates	0.996373	0.996373
spikein_reads	6,462	4,836
percent_spikeins	0.00015	0.00011
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2703	2704

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
IGHMBP2-BGRSDLV02-39dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2703	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	8772
IGHMBP2-BGRSDLV02-39dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2703	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	8848
IGHMBP2-BGRSDLV02-39dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-39dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9337
IGHMBP2-BGRSDLV02-39dox_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	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox/Aligned.sortedByCoord.out.bam		ENCORE2	9413
IGHMBP2-BGRSDLV02-39dox_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	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox/Aligned.sortedByCoord.out.bam		ENCORE2	9489
IGHMBP2-BGRSDLV02-39dox_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	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox/Aligned.sortedByCoord.out.bam		ENCORE2	9565
IGHMBP2-BGRSDLV02-39dox_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	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox/Aligned.sortedByCoord.out.bam		ENCORE2	9641
IGHMBP2-BGRSDLV02-39dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2703					GRCh38	V40	IGHMBP2-BGRSDLV02-39dox_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-39dox_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9717
IGHMBP2-BGRSDLV02-40dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2704	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	8773
IGHMBP2-BGRSDLV02-40dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2704	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	8849
IGHMBP2-BGRSDLV02-40dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-40dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9338
IGHMBP2-BGRSDLV02-40dox_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	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox/Aligned.sortedByCoord.out.bam		ENCORE2	9414
IGHMBP2-BGRSDLV02-40dox_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	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox/Aligned.sortedByCoord.out.bam		ENCORE2	9490
IGHMBP2-BGRSDLV02-40dox_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	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox/Aligned.sortedByCoord.out.bam		ENCORE2	9566
IGHMBP2-BGRSDLV02-40dox_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	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox/Aligned.sortedByCoord.out.bam		ENCORE2	9642
IGHMBP2-BGRSDLV02-40dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2704					GRCh38	V40	IGHMBP2-BGRSDLV02-40dox_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-40dox_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9718