RPS15 RNA-Seq in K562

General Information


RBP	RPS15
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS15-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	RPS15-BGKcLV44-57
Rep2	RPS15-BGKcLV44-58
CN1	NT-BGKcLV44-1
CN2	NT-BGKcLV44-2
Rep1_qPCR	53.2
Rep2_qPCR	50.6
Rep1_WB	62.7
Rep2_WB	52.7
Antibody Cat#	A305-041A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1607

Experiment Information (Status: Submitting)

	BGKcLV44-57	BGKcLV44-58
idx	0	0
TRCN#_or_BGC#	BGC#0000813	BGC#0000813
shRNA_or_gRNA_sequence	ACAAGCCCGTAAAGCATGGC	ACAAGCCCGTAAAGCATGGC
PAM	CGG	CGG
Name	RPS15-64	RPS15-64
Sample_ID	BGKcLV44-57	BGKcLV44-58
transduction_Date	7/30/24	7/30/24
days	D6	D6
RBP_name	RPS15	RPS15
qPCR_result	53.2	50.6
Ave_qPCR	51.9
RT-qPCR_primer-F	gaagtggtgaagacgcacct
RT-qPCR_primer-R	caggtagtggccgatcatct
protein_conc	4227	4164
WB_result	62.7	52.7
Ave_WB	57.7
WB_DONE_date	8/19/24
MW	17KD
IP
antibody_Cat#	A305-041A	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	5940	5941

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS15	Product_ID: A305-041A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS15-human

Experiment Status

	BGKcLV44-57	BGKcLV44-58
Sample_ID	BGKcLV44-57	BGKcLV44-58
Sample Name
Sample Name	RPS15-BGKcLV44-57	RPS15-BGKcLV44-58
RBP	RPS15	RPS15
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13606	13607

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV44-57	BGKcLV44-58
Sample #	35	36
Sample Name	RPS15-BGKcLV44-57	RPS15-BGKcLV44-58
Sample_Name_Alias
Index Well Position	C10	D10
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	293	291
Peak_Molarity	97.50	85.50
libSampleQC_DNA_Well	DNA_Library_set75/set1/C10.png	DNA_Library_set75/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set75/set1/C4.png	RNA_Library_set75/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-15	2024-10-15
Sample_ID	BGKcLV44-57	BGKcLV44-58
RBP	RPS15	RPS15
Batch_ID	BGKcLV44	BGKcLV44
WB_result	62.700	52.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4594	4595

Sequencing Information

	BGKcLV44-57	BGKcLV44-58
Sample_ID	BGKcLV44-57	BGKcLV44-58
Sample Name	RPS15-BGKcLV44-57	RPS15-BGKcLV44-58
Pool ID	Pool-241015	Pool-241015
LocalServer_folder	set75	set75
total_reads	51,143,414	50,179,129
total_aligned_reads	48,845,181	47,968,322
unique_aligned_reads	45,389,470	44,094,324
percent_uniqueAligned	0.88749	0.87874
correlation_replicates	0.992628	0.992628
spikein_reads	69,666	54,708
percent_spikeins	0.00136	0.00109
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3305	3306

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
RPS15-BGKcLV44-57_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3305	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	30964
RPS15-BGKcLV44-57_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3305	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	31006
RPS15-BGKcLV44-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3305					GRCh38	V40	RPS15-BGKcLV44-57_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGKcLV44-57_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31048
RPS15-BGKcLV44-57_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	3305					GRCh38	V40	RPS15-BGKcLV44-57_Aligned.sortedByCoord.out.bam		ENCORE2	31090
RPS15-BGKcLV44-57_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	3305					GRCh38	V40	RPS15-BGKcLV44-57_Aligned.sortedByCoord.out.bam		ENCORE2	31132
RPS15-BGKcLV44-57_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	3305					GRCh38	V40	RPS15-BGKcLV44-57_Aligned.sortedByCoord.out.bam		ENCORE2	31174
RPS15-BGKcLV44-57_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	3305					GRCh38	V40	RPS15-BGKcLV44-57_Aligned.sortedByCoord.out.bam		ENCORE2	31216
RPS15-BGKcLV44-57_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3305					GRCh38	V40	RPS15-BGKcLV44-57_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGKcLV44-57_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31258
RPS15-BGKcLV44-58_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3306	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	30965
RPS15-BGKcLV44-58_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set75/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3306	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	31007
RPS15-BGKcLV44-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set75/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3306					GRCh38	V40	RPS15-BGKcLV44-58_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGKcLV44-58_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31049
RPS15-BGKcLV44-58_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	3306					GRCh38	V40	RPS15-BGKcLV44-58_Aligned.sortedByCoord.out.bam		ENCORE2	31091
RPS15-BGKcLV44-58_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	3306					GRCh38	V40	RPS15-BGKcLV44-58_Aligned.sortedByCoord.out.bam		ENCORE2	31133
RPS15-BGKcLV44-58_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	3306					GRCh38	V40	RPS15-BGKcLV44-58_Aligned.sortedByCoord.out.bam		ENCORE2	31175
RPS15-BGKcLV44-58_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	3306					GRCh38	V40	RPS15-BGKcLV44-58_Aligned.sortedByCoord.out.bam		ENCORE2	31217
RPS15-BGKcLV44-58_quant.sf	ENCODE_DATA/set75/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3306					GRCh38	V40	RPS15-BGKcLV44-58_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGKcLV44-58_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31259