RBM12 RNA-Seq in K562

General Information


RBP	RBM12
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM12-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RBM12-BGKcLV46-53
Rep2	RBM12-BGKcLV46-54
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	10.1
Rep2_qPCR	17.4
Rep1_WB
Rep2_WB
Antibody Cat#	A301-198A
Antibody Lot#
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1645

Experiment Information (Status: Submitting)

	BGKcLV46-53	BGKcLV46-54
idx	0	0
TRCN#_or_BGC#	BGC#0001251	BGC#0001251
shRNA_or_gRNA_sequence	GGGCCACTTCCAAACCCCGG	GGGCCACTTCCAAACCCCGG
PAM	GGG	GGG
Name	RBM12_85	RBM12_85
Sample_ID	BGKcLV46-53	BGKcLV46-54
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RBM12	RBM12
qPCR_result	10.1	17.4
Ave_qPCR	13.8
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3178	3397
WB_result
Ave_WB
WB_DONE_date	1/2/24,1/6/25	need discussion
MW	97kd
IP
antibody_Cat#	A301-198A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note	check result befor release	check result befor release
ID	6049	6050

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-53	BGKcLV46-54
Sample_ID	BGKcLV46-53	BGKcLV46-54
Sample Name
Sample Name	RBM12-BGKcLV46-53	RBM12-BGKcLV46-54
RBP	RBM12	RBM12
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14044	14045

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-53	BGKcLV46-54
Sample #	23	24
Sample Name	RBM12-BGKcLV46-53	RBM12-BGKcLV46-54
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	300	300
Peak_Molarity	55.40	64.70
libSampleQC_DNA_Well	DNA_Library_set77/set1/G9.png	DNA_Library_set77/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/G3.png	RNA_Library_set77/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-53	BGKcLV46-54
RBP	RBM12	RBM12
Batch_ID	BGKcLV46	BGKcLV46
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4682	4683

Sequencing Information

	BGKcLV46-53	BGKcLV46-54
Sample_ID	BGKcLV46-53	BGKcLV46-54
Sample Name	RBM12-BGKcLV46-53	RBM12-BGKcLV46-54
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	64,031,440	66,472,699
total_aligned_reads	58,295,253	61,903,758
unique_aligned_reads	53,688,356	57,058,864
percent_uniqueAligned	0.83847	0.85838
correlation_replicates	0.984645	0.984645
spikein_reads	110,970	200,818
percent_spikeins	0.00173	0.00302
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3387	3388

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
RBM12-BGKcLV46-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3387	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32172
RBM12-BGKcLV46-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3387	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32222
RBM12-BGKcLV46-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM12-BGKcLV46-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32272
RBM12-BGKcLV46-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_Aligned.sortedByCoord.out.bam		ENCORE2	32322
RBM12-BGKcLV46-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_Aligned.sortedByCoord.out.bam		ENCORE2	32372
RBM12-BGKcLV46-53_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_Aligned.sortedByCoord.out.bam		ENCORE2	32422
RBM12-BGKcLV46-53_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_Aligned.sortedByCoord.out.bam		ENCORE2	32472
RBM12-BGKcLV46-53_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3387					GRCh38	V40	RBM12-BGKcLV46-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM12-BGKcLV46-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32522
RBM12-BGKcLV46-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3388	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32173
RBM12-BGKcLV46-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3388	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32223
RBM12-BGKcLV46-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM12-BGKcLV46-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32273
RBM12-BGKcLV46-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_Aligned.sortedByCoord.out.bam		ENCORE2	32323
RBM12-BGKcLV46-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_Aligned.sortedByCoord.out.bam		ENCORE2	32373
RBM12-BGKcLV46-54_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_Aligned.sortedByCoord.out.bam		ENCORE2	32423
RBM12-BGKcLV46-54_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_Aligned.sortedByCoord.out.bam		ENCORE2	32473
RBM12-BGKcLV46-54_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3388					GRCh38	V40	RBM12-BGKcLV46-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM12-BGKcLV46-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32523