RPS15A RNA-Seq in K562

General Information


RBP	RPS15A
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS15A-BGKcLV30-K562
ENCODE_series_ID	ENCSR227MBD
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR292NHK
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RPS15A-BGKcLV30-67
Rep2	RPS15A-BGKcLV30-68
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	25.1
Rep2_qPCR	28.0
Rep1_WB	51.4
Rep2_WB	55.7
Antibody Cat#	A304-990A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB489CNK
Status	Submitted
Project	ENCODE4
ID	879

Experiment Information (Status: Released)

	BGKcLV30-67	BGKcLV30-68
idx	1096	1097
TRCN#_or_BGC#	BGC#0000814	BGC#0000814
shRNA_or_gRNA_sequence	ACTTACCCAAACTGGCGGGA	ACTTACCCAAACTGGCGGGA
PAM	TGG	TGG
Name	RPS15A-90	RPS15A-90
Sample_ID	BGKcLV30-67	BGKcLV30-68
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RPS15A	RPS15A
qPCR_result	25.1	28.0
Ave_qPCR	26.6
RT-qPCR_primer-F	tggcgaatttgaaatcattg
RT-qPCR_primer-R	ttctgccatttttccaggtc
protein_conc	2284	2400
WB_result	51.4	55.7
Ave_WB	53.6
WB_DONE_date	9/13/21
MW	15KD
IP
antibody_Cat#	A304-990A	LOT #1
Antibody DCC ID	ENCAB489CNK
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/10/21	11/10/21
repeat_library
Note
ID	5236	5237

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS15A	Product_ID: A304-990A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS15A-human

Experiment Status

	BGKcLV30-67	BGKcLV30-68
Sample_ID	BGKcLV30-67	BGKcLV30-68
Sample Name
Sample Name	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-68
RBP	RPS15A	RPS15A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10083	10084

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-67	BGKcLV30-68
Sample #	73	74
Sample Name	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-68
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	278	282
Peak_Molarity	54.80	52.50
libSampleQC_DNA_Well	DNA_Library_set50/set2/E12.png	DNA_Library_set50/set2/F12.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set50/set2/E12.png	RNA_Library_set50/set2/F12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-67	BGKcLV30-68
RBP	RPS15A	RPS15A
Batch_ID	BGKcLV30	BGKcLV30
WB_result	51.400	55.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3160	3161

Sequencing Information

	BGKcLV30-67	BGKcLV30-68
Sample_ID	BGKcLV30-67	BGKcLV30-68
Sample Name	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-68
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	96,897,568	82,339,820
total_aligned_reads	91,766,360	78,430,026
unique_aligned_reads	83,757,728	71,726,046
percent_uniqueAligned	0.86439	0.87110
correlation_replicates	0.995886	0.995886
spikein_reads	8,952	6,330
percent_spikeins	0.00009	0.00008
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1945	1946

Data Submission Information

	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-68	BGKcLV30-68	BGKcLV30-68	BGKcLV30-68
ENCODE_alias	brenton-graveley:RPS15A-BGKcLV30	brenton-graveley:RPS15A-BGKcLV30-67	brenton-graveley:L-RPS15A-BGKcLV30-67	brenton-graveley:RPS15A-BGKcLV30-67_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGKcLV30-67_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGKcLV30-K562	brenton-graveley:RPS15A-BGKcLV30-68	brenton-graveley:L-RPS15A-BGKcLV30-68	brenton-graveley:RPS15A-BGKcLV30-68_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGKcLV30-68_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR292NHK	ENCBS618IFP	ENCLB840JDC	ENCFF082RKE	ENCFF122HOT	ENCSR227MBD	ENCBS425RTI	ENCLB212FWY	ENCFF539DWA	ENCFF075INM
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-67	BGKcLV30-68	BGKcLV30-68	BGKcLV30-68	BGKcLV30-68
Sample Name	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-67	RPS15A-BGKcLV30-68	RPS15A-BGKcLV30-68	RPS15A-BGKcLV30-68	RPS15A-BGKcLV30-68
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RPS15A-BGKcLV30-67.pdf	L-RPS15A-BGKcLV30-67.pdf				RPS15A-BGKcLV30-68.pdf	L-RPS15A-BGKcLV30-68.pdf
ID	5878	5949	6021	6093	6165	6200	5950	6022	6094	6166

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
RPS15A-BGKcLV30-67_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1945	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5873
RPS15A-BGKcLV30-67_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1945	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5903
RPS15A-BGKcLV30-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGKcLV30-67_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18774
RPS15A-BGKcLV30-67_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67/Aligned.sortedByCoord.out.bam		ENCORE2	18804
RPS15A-BGKcLV30-67_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67/Aligned.sortedByCoord.out.bam		ENCORE2	18834
RPS15A-BGKcLV30-67_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67/Aligned.sortedByCoord.out.bam		ENCORE2	18864
RPS15A-BGKcLV30-67_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67/Aligned.sortedByCoord.out.bam		ENCORE2	18894
RPS15A-BGKcLV30-67_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1945					GRCh38	V40	RPS15A-BGKcLV30-67_S75_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGKcLV30-67_S75_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18924
RPS15A-BGKcLV30-68_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1946	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5874
RPS15A-BGKcLV30-68_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1946	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5904
RPS15A-BGKcLV30-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGKcLV30-68_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18775
RPS15A-BGKcLV30-68_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68/Aligned.sortedByCoord.out.bam		ENCORE2	18805
RPS15A-BGKcLV30-68_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68/Aligned.sortedByCoord.out.bam		ENCORE2	18835
RPS15A-BGKcLV30-68_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68/Aligned.sortedByCoord.out.bam		ENCORE2	18865
RPS15A-BGKcLV30-68_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68/Aligned.sortedByCoord.out.bam		ENCORE2	18895
RPS15A-BGKcLV30-68_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1946					GRCh38	V40	RPS15A-BGKcLV30-68_S76_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGKcLV30-68_S76_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18925