RBM42 RNA-Seq in K562

General Information


RBP	RBM42
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM42-BGKcLV51-K562
ENCODE_series_ID
Batch_ID	BGKcLV51
Pool ID	Pool-260528
Local_Set_Name	set82
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBM42-BGKcLV51-81
Rep2	RBM42-BGKcLV51-82
CN1	NT-BGKcLV51-1
CN2	NT-BGKcLV51-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	54.3
Rep2_WB	49.7
Antibody Cat#	A305-138A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1721

Experiment Information (Status: Submitting)

	BGKcLV51-81	BGKcLV51-82
idx	0	0
TRCN#_or_BGC#	BGC#0001364	BGC#0001364
shRNA_or_gRNA_sequence	TGTTGGTCGCGATAATTGGG	TGTTGGTCGCGATAATTGGG
PAM	CGG	CGG
Name	RBM42_93	RBM42_93
Sample_ID	BGKcLV51-81	BGKcLV51-82
transduction_Date	9/30/2025	9/30/2025
days	D6	D6
RBP_name	RBM42	RBM42
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	atgatgctgccaccaatg
RT-qPCR_primer-R	caccactgcctcttccttct
protein_conc	2257	2267
WB_result	54.3	49.7
Ave_WB
WB_DONE_date	10/15/25,10/14/25
MW	50KD
IP
antibody_Cat#	A305-138A	lot# 1
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	6322	6323

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM42	Product_ID: A305-139A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM42-human

Experiment Status

	BGKcLV51-81	BGKcLV51-82
Sample_ID	BGKcLV51-81	BGKcLV51-82
Sample Name
Sample Name	RBM42-BGKcLV51-81	RBM42-BGKcLV51-82
RBP	RBM42	RBM42
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2026-10-30	2026-10-30
Project	ENCORE2	ENCORE2
Note
ID	14578	14579

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV51-81	BGKcLV51-82
Sample #	13	14
Sample Name	RBM42-BGKcLV51-81	RBM42-BGKcLV51-82
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2026-05-18	2026-05-18
Lib_ID	Lib-260518	Lib-260518
Tecan_Location
Tecan
Tecan_date
Size_bp	288	289
Peak_Molarity	53.10	70.20
libSampleQC_DNA_Well	DNA_Library_set82/set1/E9.png	DNA_Library_set82/set1/F9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set82/set1/E2.png	RNA_Library_set82/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2026-05-21	2026-05-21
Sample_ID	BGKcLV51-81	BGKcLV51-82
RBP	RBM42	RBM42
Batch_ID	BGKcLV51	BGKcLV51
WB_result	54.300	49.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4852	4853

Sequencing Information

	BGKcLV51-81	BGKcLV51-82
Sample_ID	BGKcLV51-81	BGKcLV51-82
Sample Name	RBM42-BGKcLV51-81	RBM42-BGKcLV51-82
Pool ID	Pool-260528	Pool-260528
LocalServer_folder	set82	set82
total_reads	37,275,182	28,084,011
total_aligned_reads	32,514,280	23,809,459
unique_aligned_reads	30,407,760	22,257,063
percent_uniqueAligned	0.81576	0.79252
correlation_replicates	0.996459	0.996459
spikein_reads	88,800	67,204
percent_spikeins	0.00238	0.00239
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	3553	3554

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
RBM42-BGKcLV51-81_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3553	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33684
RBM42-BGKcLV51-81_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3553	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33742
RBM42-BGKcLV51-81_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_R1.filtered.trimmed.paired.fastq.gz,RBM42-BGKcLV51-81_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33802
RBM42-BGKcLV51-81_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_Aligned.sortedByCoord.out.bam		ENCORE2	33860
RBM42-BGKcLV51-81_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_Aligned.sortedByCoord.out.bam		ENCORE2	33918
RBM42-BGKcLV51-81_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_Aligned.sortedByCoord.out.bam		ENCORE2	33976
RBM42-BGKcLV51-81_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_Aligned.sortedByCoord.out.bam		ENCORE2	34034
RBM42-BGKcLV51-81_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3553					GRCh38	V40	RBM42-BGKcLV51-81_R1.filtered.trimmed.paired.fastq.gz,RBM42-BGKcLV51-81_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34092
RBM42-BGKcLV51-82_R1.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3554	NovaSeq6000	100	paired-ended	1				NT-BGKcLV51-1_R1.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R1.filtered.trimmed.paired.fastq.gz	ENCORE2	33685
RBM42-BGKcLV51-82_R2.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set82/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3554	NovaSeq6000	100	paired-ended	2				NT-BGKcLV51-1_R2.filtered.trimmed.paired.fastq.gz,NT-BGKcLV51-2_R2.filtered.trimmed.paired.fastq.gz	ENCORE2	33743
RBM42-BGKcLV51-82_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_R1.filtered.trimmed.paired.fastq.gz,RBM42-BGKcLV51-82_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	33803
RBM42-BGKcLV51-82_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_Aligned.sortedByCoord.out.bam		ENCORE2	33861
RBM42-BGKcLV51-82_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_Aligned.sortedByCoord.out.bam		ENCORE2	33919
RBM42-BGKcLV51-82_Signal.Unique.strand-.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_Aligned.sortedByCoord.out.bam		ENCORE2	33977
RBM42-BGKcLV51-82_Signal.Unique.strand+.bw	ENCODE_DATA/set82/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_Aligned.sortedByCoord.out.bam		ENCORE2	34035
RBM42-BGKcLV51-82_quant.sf	ENCODE_DATA/set82/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3554					GRCh38	V40	RBM42-BGKcLV51-82_R1.filtered.trimmed.paired.fastq.gz,RBM42-BGKcLV51-82_R2.filtered.trimmed.paired.fastq.gz		ENCORE2	34093