RPS3 RNA-Seq in K562

General Information


RBP	RPS3
Cell_Line	K562
Method	shRNA
Exp_Name	RPS3-BGKLV13-K562
ENCODE_series_ID
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR410MIQ
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	RPS3_BGKLV13_65
Rep2	RPS3_BGKLV13_66
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	83.8
Rep2_qPCR	82.5
Rep1_WB	20.2
Rep2_WB	27.9
Antibody Cat#	A303-840A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB855QRN
Status	Archived
Project	ENCODE3
ID	380

Experiment Information (Status: Released)

	BGKLV13-65	BGKLV13-66
idx	200	201
TRCN#_or_BGC#	TRCN0000005165	TRCN0000005165
shRNA_or_gRNA_sequence	GCCACCAGAACACAGAATGTT	GCCACCAGAACACAGAATGTT
PAM
Name	RPS3	RPS3
Sample_ID	BGKLV13-65	BGKLV13-66
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	RPS3	RPS3
qPCR_result	83.8	82.5
Ave_qPCR	83.2
RT-qPCR_primer-F	GTGCGAGTTACACCAACCAG
RT-qPCR_primer-R	ACAGCAGTCAGTTCCCGAAT
protein_conc	2080	2098
WB_result	20.2	27.9
Ave_WB	24.1
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A303-840A	A303-840A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	539.15817	0
Rep2_TPM	694.501278	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	219	220

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-65	BGKLV13-66
Sample_ID	BGKLV13-65	BGKLV13-66
Sample Name	RPS3_BGKLV13_65	RPS3_BGKLV13_66
Sample Name	RPS3_BGKLV13_65	RPS3_BGKLV13_66
RBP	RPS3	RPS3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	468	469

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-65	BGKLV13-66
Sample #
Sample Name	RPS3-BGKLV13-65	RPS3-BGKLV13-66
Sample_Name_Alias	RPS3_BGKLV13_65	RPS3_BGKLV13_66
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F6.png	DNA_Library_LV13-14/set1/G6.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A3.png	RNA_Library_LV13-14-16/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-65	BGKLV13-66
RBP	RPS3	RPS3
Batch_ID	BGKLV13	BGKLV13
WB_result	20.200	27.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2164	2165

Sequencing Information

	BGKLV13-65	BGKLV13-66
Sample_ID	BGKLV13-65	BGKLV13-66
Sample Name	RPS3_BGKLV13_65	RPS3_BGKLV13_66
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	40,980,000	32,990,000
total_aligned_reads	39,111,014	31,850,522
unique_aligned_reads	35,843,698	29,163,684
percent_uniqueAligned	0.87466	0.88402
correlation_replicates	0.998742	0.998742
spikein_reads	139,966	116,232
percent_spikeins	0.00342	0.00352
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	806	807

Data Submission Information

	BGKLV13-65
ENCODE_alias	brenton-graveley:RPS3_BGKLV13
ENCODE_accession	ENCSR410MIQ
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV13-65
Sample Name	RPS3_BGKLV13_65
Selected	Yes
Status	Released
Status_Date	2014-10-15
Project	ENCODE3

protocol_URL
ID	2783

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
RPS3_BGKLV13_65_CGTACG_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	806	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13396
RPS3_BGKLV13_65_CGTACG_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	806	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13448
RPS3_BGKLV13_65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65_CGTACG_L007_R1_001.fastq.gz,RPS3_BGKLV13_65_CGTACG_L007_R2_001.fastq.gz		ENCORE2	13500
RPS3_BGKLV13_65_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65/Aligned.sortedByCoord.out.bam		ENCORE2	13552
RPS3_BGKLV13_65_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65/Aligned.sortedByCoord.out.bam		ENCORE2	13604
RPS3_BGKLV13_65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65/Aligned.sortedByCoord.out.bam		ENCORE2	13656
RPS3_BGKLV13_65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65/Aligned.sortedByCoord.out.bam		ENCORE2	13708
RPS3_BGKLV13_65_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	806					GRCh38	V40	RPS3_BGKLV13_65_CGTACG_L007_R1_001.fastq.gz,RPS3_BGKLV13_65_CGTACG_L007_R2_001.fastq.gz		ENCORE2	13760
RPS3_BGKLV13_66_GAGTGG_L007_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	807	HiSeq2000	100	paired-ended	1				non-target_BGKLV13_73_GATCAG_L005_R1_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	13397
RPS3_BGKLV13_66_GAGTGG_L007_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	807	HiSeq2000	100	paired-ended	2				non-target_BGKLV13_73_GATCAG_L005_R2_001.fastq.gz,non-target_BGKLV13_74_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	13449
RPS3_BGKLV13_66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66_GAGTGG_L007_R1_001.fastq.gz,RPS3_BGKLV13_66_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	13501
RPS3_BGKLV13_66_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66/Aligned.sortedByCoord.out.bam		ENCORE2	13553
RPS3_BGKLV13_66_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66/Aligned.sortedByCoord.out.bam		ENCORE2	13605
RPS3_BGKLV13_66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66/Aligned.sortedByCoord.out.bam		ENCORE2	13657
RPS3_BGKLV13_66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66/Aligned.sortedByCoord.out.bam		ENCORE2	13709
RPS3_BGKLV13_66_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	807					GRCh38	V40	RPS3_BGKLV13_66_GAGTGG_L007_R1_001.fastq.gz,RPS3_BGKLV13_66_GAGTGG_L007_R2_001.fastq.gz		ENCORE2	13761