RBM5 RNA-Seq in K562

General Information


RBP	RBM5
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM5-BGKcLV44-K562
ENCODE_series_ID
Batch_ID	BGKcLV44
Pool ID	Pool-241015
Local_Set_Name	set75
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBM5-BGKcLV44-99
Rep2	RBM5-BGKcLV44-100
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	63.7
Rep2_WB	53.5
Antibody Cat#	86425S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1614

Experiment Information (Status: Submitting)

	BGKcLV44-99	BGKcLV44-100
idx	0	0
TRCN#_or_BGC#	BGC#0000042	BGC#0000042
shRNA_or_gRNA_sequence	ACTATGGTGAGCACGACTAT	ACTATGGTGAGCACGACTAT
PAM
Name	RBM5_4-F	RBM5_4-F
Sample_ID	BGKcLV44-99	BGKcLV44-100
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	RBM5	RBM5
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CCTTAGCTGAAAGGCAGCAG
RT-qPCR_primer-R	CACCAGCTCCTCCTCATTGT
protein_conc	4674	4710
WB_result	63.7	53.5
Ave_WB	58.6
WB_DONE_date	8/22/24,8/28/24
MW	92kDa
IP
antibody_Cat#	86425S	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	5982	5983

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM5	Product_ID: 86425S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RBM5-human

Experiment Status

	BGKcLV44-99	BGKcLV44-100
Sample_ID	BGKcLV44-99	BGKcLV44-100
Sample Name
Sample Name	RBM5-BGKcLV44-99	RBM5-BGKcLV44-100
RBP	RBM5	RBM5
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13620	13621

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-99	BGKcLV44-100
Sample #	49	50
Sample Name	RBM5-BGKcLV44-99	RBM5-BGKcLV44-100
Sample_Name_Alias
Index Well Position	A12	B12
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-10	2024-10-10
Lib_ID	Lib-241010	Lib-241010
Tecan_Location
Tecan
Tecan_date
Size_bp	286	278
Peak_Molarity	68.10	95.40
libSampleQC_DNA_Well	DNA_Library_set75/set1/A12.png	DNA_Library_set75/set1/B12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/A6.png	RNA_Library_set75/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-99	BGKcLV44-100
RBP	RBM5	RBM5
Batch_ID	BGKcLV44	BGKcLV44
WB_result	63.700	53.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4608	4609

Sequencing Information

	BGKcLV44-99	BGKcLV44-100
Sample_ID	BGKcLV44-99	BGKcLV44-100
Sample Name	RBM5-BGKcLV44-99	RBM5-BGKcLV44-100
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	46,046,134	52,381,057
total_aligned_reads	43,375,271	49,991,480
unique_aligned_reads	39,841,318	46,059,836
percent_uniqueAligned	0.86525	0.87932
correlation_replicates	0.972234	0.972234
spikein_reads	71,722	62,334
percent_spikeins	0.00156	0.00119
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3319	3320

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
RBM5-BGKcLV44-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3319	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30963
RBM5-BGKcLV44-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3319	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31005
RBM5-BGKcLV44-99_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGKcLV44-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31047
RBM5-BGKcLV44-99_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_Aligned.sortedByCoord.out.bam		ENCORE2	31089
RBM5-BGKcLV44-99_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_Aligned.sortedByCoord.out.bam		ENCORE2	31131
RBM5-BGKcLV44-99_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_Aligned.sortedByCoord.out.bam		ENCORE2	31173
RBM5-BGKcLV44-99_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_Aligned.sortedByCoord.out.bam		ENCORE2	31215
RBM5-BGKcLV44-99_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3319					GRCh38	V40	RBM5-BGKcLV44-99_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGKcLV44-99_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31257
RBM5-BGKcLV44-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3320	NovaSeq6000	100	paired-ended	1				NT-BGKcLV44-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30962
RBM5-BGKcLV44-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3320	NovaSeq6000	100	paired-ended	2				NT-BGKcLV44-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV44-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31004
RBM5-BGKcLV44-100_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGKcLV44-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31046
RBM5-BGKcLV44-100_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_Aligned.sortedByCoord.out.bam		ENCORE2	31088
RBM5-BGKcLV44-100_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_Aligned.sortedByCoord.out.bam		ENCORE2	31130
RBM5-BGKcLV44-100_Signal.Unique.strand-.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_Aligned.sortedByCoord.out.bam		ENCORE2	31172
RBM5-BGKcLV44-100_Signal.Unique.strand+.bw	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_Aligned.sortedByCoord.out.bam		ENCORE2	31214
RBM5-BGKcLV44-100_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3320					GRCh38	V40	RBM5-BGKcLV44-100_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM5-BGKcLV44-100_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31256