IGHMBP2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Released)

	BGRSDLV02-37	BGRSDLV02-38
idx	0	0
TRCN#_or_BGC#	TRCN0000019160	TRCN0000019160
shRNA_or_gRNA_sequence	CCGGCCTTTGAGTATCTTGACGATACTCGAGTATCGTCAAGATACTCAAAGGTTTTT	CCGGCCTTTGAGTATCTTGACGATACTCGAGTATCGTCAAGATACTCAAAGGTTTTT
PAM
Name	IGHMBP2	IGHMBP2
Sample_ID	BGRSDLV02-37	BGRSDLV02-38
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	IGHMBP2	IGHMBP2
qPCR_result	90.0	87.5
Ave_qPCR	88.7
RT-qPCR_primer-F	gagagaaggaggccgtgata
RT-qPCR_primer-R	ggtcctcagcaagaaaacca
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	11296	11297

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-37	BGRSDLV02-38
Sample_ID	BGRSDLV02-37	BGRSDLV02-38
Sample Name
Sample Name	IGHMBP2-BGRSDLV02-37	IGHMBP2-BGRSDLV02-38
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	12352	12353

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-37	BGRSDLV02-38
Sample #	33	34
Sample Name	IGHMBP2-BGRSDLV02-37	IGHMBP2-BGRSDLV02-38
Sample_Name_Alias
Index Well Position	A05	B05
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	295	294
Peak_Molarity	88.00	93.10
libSampleQC_DNA_Well	DNA_Library_set65/set1/A5.png	DNA_Library_set65/set1/B5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/A5.png	RNA_Library_set65/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-37	BGRSDLV02-38
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	3954	3955

Sequencing Information

	BGRSDLV02-37	BGRSDLV02-38
Sample_ID	BGRSDLV02-37	BGRSDLV02-38
Sample Name	IGHMBP2-BGRSDLV02-37	IGHMBP2-BGRSDLV02-38
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	41,723,947	25,866,209
total_aligned_reads	39,241,656	24,097,871
unique_aligned_reads	36,605,043	22,541,980
percent_uniqueAligned	0.87731	0.87148
correlation_replicates	0.997019	0.997019
spikein_reads	15,170	3,870
percent_spikeins	0.00036	0.00015
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2701	2702

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-BGRSDLV02-37_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2701	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8770
IGHMBP2-BGRSDLV02-37_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2701	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8846
IGHMBP2-BGRSDLV02-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-37_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9335
IGHMBP2-BGRSDLV02-37_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	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37/Aligned.sortedByCoord.out.bam		ENCORE2	9411
IGHMBP2-BGRSDLV02-37_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	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37/Aligned.sortedByCoord.out.bam		ENCORE2	9487
IGHMBP2-BGRSDLV02-37_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	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37/Aligned.sortedByCoord.out.bam		ENCORE2	9563
IGHMBP2-BGRSDLV02-37_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	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37/Aligned.sortedByCoord.out.bam		ENCORE2	9639
IGHMBP2-BGRSDLV02-37_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2701					GRCh38	V40	IGHMBP2-BGRSDLV02-37_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-37_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9715
IGHMBP2-BGRSDLV02-38_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2702	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8771
IGHMBP2-BGRSDLV02-38_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2702	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8847
IGHMBP2-BGRSDLV02-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-38_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9336
IGHMBP2-BGRSDLV02-38_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	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38/Aligned.sortedByCoord.out.bam		ENCORE2	9412
IGHMBP2-BGRSDLV02-38_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	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38/Aligned.sortedByCoord.out.bam		ENCORE2	9488
IGHMBP2-BGRSDLV02-38_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	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38/Aligned.sortedByCoord.out.bam		ENCORE2	9564
IGHMBP2-BGRSDLV02-38_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	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38/Aligned.sortedByCoord.out.bam		ENCORE2	9640
IGHMBP2-BGRSDLV02-38_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2702					GRCh38	V40	IGHMBP2-BGRSDLV02-38_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,IGHMBP2-BGRSDLV02-38_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9716