RPS3A RNA-Seq in K562

General Information


RBP	RPS3A
Cell_Line	K562
Method	shRNA
Exp_Name	RPS3A-BGKLV24-K562
ENCODE_series_ID	ENCSR803YTK
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR788YGG
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	RPS3A_BGKLV24_49B
Rep2	RPS3A_BGKLV24_50B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	77.1
Rep2_qPCR	96.8
Rep1_WB	61.2
Rep2_WB	65.1
Antibody Cat#	GTX105020
Antibody Lot#	GTX105020
Antibody DCC ID	ENCAB550TJZ
Status	Released
Project	ENCODE3
ID	608

Experiment Information (Status: Released)

	BGKLV24-49	BGKLV24-50
idx	386	387
TRCN#_or_BGC#	TRCN0000074709	TRCN0000074709
shRNA_or_gRNA_sequence	CCGGAAGAAGATGATGGAAAT	CCGGAAGAAGATGATGGAAAT
PAM
Name	RPS3A	RPS3A
Sample_ID	BGKLV24-49	BGKLV24-50
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	RPS3A	RPS3A
qPCR_result	77.1	96.8
Ave_qPCR	87.0
RT-qPCR_primer-F	caaaaagggagccaagaaga
RT-qPCR_primer-R	gtgacgagcgtctttccaat
protein_conc	3179	3659
WB_result	61.2	65.1
Ave_WB	63.1
WB_DONE_date	5/4/15/2015
MW	30kDa
IP	1	1
antibody_Cat#	GTX105020	GTX105020
Antibody DCC ID	ENCAB550TJZ	ENCAB550TJZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	463.445508	0
Rep2_TPM	558.664774	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	445	446

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS3A	Product_ID: GTX105020 Lot_ID: 39953 Source: GeneTex Target Name: RPS3A-human

Experiment Status

	BGKLV24-49	BGKLV24-50
Sample_ID	BGKLV24-49	BGKLV24-50
Sample Name	RPS3A_BGKLV24_49B	RPS3A_BGKLV24_50B
Sample Name	RPS3A_BGKLV24_49B	RPS3A_BGKLV24_50B
RBP	RPS3A	RPS3A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	898	899

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-49	BGKLV24-50
Sample #
Sample Name	RPS3A-BGKLV24-49B	RPS3A-BGKLV24-50B
Sample_Name_Alias	RPS3A_BGKLV24_49B	RPS3A_BGKLV24_50B
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G6.png	DNA_Library_LV24-25-26/set1/H6.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G5.png	RNA_Library_LV20-22-24/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-49	BGKLV24-50
RBP	RPS3A	RPS3A
Batch_ID	BGKLV24	BGKLV24
WB_result	61.200	65.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2586	2587

Sequencing Information

	BGKLV24-49	BGKLV24-50
Sample_ID	BGKLV24-49	BGKLV24-50
Sample Name	RPS3A_BGKLV24_49B	RPS3A_BGKLV24_50B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	65,211,818	86,433,698
total_aligned_reads	63,873,970	83,320,146
unique_aligned_reads	58,168,996	75,649,204
percent_uniqueAligned	0.89200	0.87523
correlation_replicates	0.995827	0.995827
spikein_reads	200,042	225,610
percent_spikeins	0.00307	0.00261
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1228	1229

Data Submission Information

	BGKLV24-49	BGKLV24-49
ENCODE_alias	brenton-graveley:RPS3A_BGKLV24_B	brenton-graveley:RPS3A-BGKLV24-K562
ENCODE_accession	ENCSR788YGG	ENCSR803YTK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-49	BGKLV24-49
Sample Name	RPS3A_BGKLV24_49B	RPS3A_BGKLV24_49B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2998	6921

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
RPS3A_BGKLV24_49B_ATGTCA_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1228	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17484
RPS3A_BGKLV24_49B_ATGTCA_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1228	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17508
RPS3A_BGKLV24_49B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B_ATGTCA_L003_001.R1.fastq.gz,RPS3A_BGKLV24_49B_ATGTCA_L003_001.R2.fastq.gz		ENCORE2	17532
RPS3A_BGKLV24_49B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B/Aligned.sortedByCoord.out.bam		ENCORE2	17556
RPS3A_BGKLV24_49B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B/Aligned.sortedByCoord.out.bam		ENCORE2	17580
RPS3A_BGKLV24_49B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B/Aligned.sortedByCoord.out.bam		ENCORE2	17604
RPS3A_BGKLV24_49B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B/Aligned.sortedByCoord.out.bam		ENCORE2	17628
RPS3A_BGKLV24_49B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1228					GRCh38	V40	RPS3A_BGKLV24_49B_ATGTCA_L003_001.R1.fastq.gz,RPS3A_BGKLV24_49B_ATGTCA_L003_001.R2.fastq.gz		ENCORE2	17652
RPS3A_BGKLV24_50B_CCGTCC_L003_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1229	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17485
RPS3A_BGKLV24_50B_CCGTCC_L003_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1229	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17509
RPS3A_BGKLV24_50B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B_CCGTCC_L003_001.R1.fastq.gz,RPS3A_BGKLV24_50B_CCGTCC_L003_001.R2.fastq.gz		ENCORE2	17533
RPS3A_BGKLV24_50B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B/Aligned.sortedByCoord.out.bam		ENCORE2	17557
RPS3A_BGKLV24_50B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B/Aligned.sortedByCoord.out.bam		ENCORE2	17581
RPS3A_BGKLV24_50B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B/Aligned.sortedByCoord.out.bam		ENCORE2	17605
RPS3A_BGKLV24_50B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B/Aligned.sortedByCoord.out.bam		ENCORE2	17629
RPS3A_BGKLV24_50B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1229					GRCh38	V40	RPS3A_BGKLV24_50B_CCGTCC_L003_001.R1.fastq.gz,RPS3A_BGKLV24_50B_CCGTCC_L003_001.R2.fastq.gz		ENCORE2	17653