RBM10 RNA-Seq in K562

General Information


RBP	RBM10
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM10-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBM10-BGKcLV42-79
Rep2	RBM10-BGKcLV42-80
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	43.1
Rep2_qPCR	28.7
Rep1_WB	need discussion
Rep2_WB
Antibody Cat#	30774S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1557

Experiment Information (Status: Submitting)

	BGKcLV42-79	BGKcLV42-79	BGKcLV42-80	BGKcLV42-80
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001179	BGC#0001179	BGC#0001179	BGC#0001179
shRNA_or_gRNA_sequence	AGTCCATGTCCCGGTAGTCG	AGTCCATGTCCCGGTAGTCG	AGTCCATGTCCCGGTAGTCG	AGTCCATGTCCCGGTAGTCG
PAM	TGG	TGG	TGG	TGG
Name	RBM10_95	RBM10_95	RBM10_95	RBM10_95
Sample_ID	BGKcLV42-79	BGKcLV42-79	BGKcLV42-80	BGKcLV42-80
transduction_Date	4/23/24	4/23/24	4/23/24	4/23/24
days	D6	D6	D6	D6
RBP_name	RBM10	RBM10	RBM10	RBM10
qPCR_result	43.1	43.1	28.7	28.7
Ave_qPCR	35.9	35.9
RT-qPCR_primer-F	ctttgccttcatccagctct	ctttgccttcatccagctct
RT-qPCR_primer-R	cccttggcaaactcaacatt	cccttggcaaactcaacatt
protein_conc	2686	2686	2670	2670
WB_result	need discussion	58.4		62.6949
Ave_WB
WB_DONE_date	5/10/24	7/23/24
MW	110,135kd	110,135kd
IP
antibody_Cat#	30774S	47729S	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note	check result befor release		check result befor release
ID	5845	5847	5846	5848

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM10	Product_ID: 47729S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RBM10-human
RBM10	Product_ID: 30774S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RBM10-human

Experiment Status

	BGKcLV42-79	BGKcLV42-80
Sample_ID	BGKcLV42-79	BGKcLV42-80
Sample Name
Sample Name	RBM10-BGKcLV42-79	RBM10-BGKcLV42-80
RBP	RBM10	RBM10
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13108	13109

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-79	BGKcLV42-80
Sample #	65	66
Sample Name	RBM10-BGKcLV42-79	RBM10-BGKcLV42-80
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	324	303
Peak_Molarity	93.60	97.90
libSampleQC_DNA_Well	DNA_Library_set73/set1/A9.png	DNA_Library_set73/set1/B9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A9.png	RNA_Library_set73/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-79	BGKcLV42-80
RBP	RBM10	RBM10
Batch_ID	BGKcLV42	BGKcLV42
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4334	4335

Sequencing Information

	BGKcLV42-79	BGKcLV42-80
Sample_ID	BGKcLV42-79	BGKcLV42-80
Sample Name	RBM10-BGKcLV42-79	RBM10-BGKcLV42-80
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	62,686,807	36,394,250
total_aligned_reads	58,515,181	32,201,235
unique_aligned_reads	54,253,446	29,764,773
percent_uniqueAligned	0.86547	0.81784
correlation_replicates	0.975690	0.975690
spikein_reads	5,790	792
percent_spikeins	0.00009	0.00002
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3201	3202

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
RBM10-BGKcLV42-79_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3201	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30404
RBM10-BGKcLV42-79_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3201	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30494
RBM10-BGKcLV42-79_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGKcLV42-79_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31336
RBM10-BGKcLV42-79_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_Aligned.sortedByCoord.out.bam		ENCORE2	31426
RBM10-BGKcLV42-79_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_Aligned.sortedByCoord.out.bam		ENCORE2	31516
RBM10-BGKcLV42-79_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_Aligned.sortedByCoord.out.bam		ENCORE2	31606
RBM10-BGKcLV42-79_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_Aligned.sortedByCoord.out.bam		ENCORE2	31696
RBM10-BGKcLV42-79_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3201					GRCh38	V40	RBM10-BGKcLV42-79_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGKcLV42-79_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31786
RBM10-BGKcLV42-80_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3202	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30405
RBM10-BGKcLV42-80_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3202	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30495
RBM10-BGKcLV42-80_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGKcLV42-80_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31337
RBM10-BGKcLV42-80_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_Aligned.sortedByCoord.out.bam		ENCORE2	31427
RBM10-BGKcLV42-80_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_Aligned.sortedByCoord.out.bam		ENCORE2	31517
RBM10-BGKcLV42-80_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_Aligned.sortedByCoord.out.bam		ENCORE2	31607
RBM10-BGKcLV42-80_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_Aligned.sortedByCoord.out.bam		ENCORE2	31697
RBM10-BGKcLV42-80_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3202					GRCh38	V40	RBM10-BGKcLV42-80_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM10-BGKcLV42-80_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31787