RPS10 RNA-Seq in K562

General Information


RBP	RPS10
Cell_Line	K562
Method	shRNA
Exp_Name	RPS10-BGKLV13-K562
ENCODE_series_ID	ENCSR819WUX
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR004RGI
ENCODE_CN_Exp_ID	ENCSR084SCN
Rep1	RPS10_BGKLV13_63
Rep2	RPS10_BGKLV13_64
CN1	non-target_BGKLV13_73
CN2	non-target_BGKLV13_74
Rep1_qPCR	63.6
Rep2_qPCR	56.4
Rep1_WB	33.7
Rep2_WB	36.3
Antibody Cat#	RN068PW
Antibody Lot#	LOT# 001
Antibody DCC ID	ENCAB563YNZ
Status	Released
Project	ENCODE3
ID	379

Experiment Information (Status: Released)

	BGKLV13-63	BGKLV13-64
idx	198	199
TRCN#_or_BGC#	TRCN0000074810	TRCN0000074810
shRNA_or_gRNA_sequence	CTGGAGACATTTCTACTGGTA	CTGGAGACATTTCTACTGGTA
PAM
Name	RPS10	RPS10
Sample_ID	BGKLV13-63	BGKLV13-64
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	RPS10	RPS10
qPCR_result	63.6	56.4
Ave_qPCR	60.0
RT-qPCR_primer-F	GGGAAGCTGACAGAGATACC
RT-qPCR_primer-R	ACTGGAATTCGGTTGCTGAC
protein_conc	2330	2125
WB_result	33.7	36.3
Ave_WB	35.0
WB_DONE_date	6/12/19
MW	19KD
IP	1	1
antibody_Cat#	RN068PW
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	137.015642	0
Rep2_TPM	140.171304	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	217	218

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-63	BGKLV13-64
Sample_ID	BGKLV13-63	BGKLV13-64
Sample Name	RPS10_BGKLV13_63	RPS10_BGKLV13_64
Sample Name	RPS10_BGKLV13_63	RPS10_BGKLV13_64
RBP	RPS10	RPS10
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	466	467

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-63	BGKLV13-64
Sample #
Sample Name	RPS10-BGKLV13-63	RPS10-BGKLV13-64
Sample_Name_Alias	RPS10_BGKLV13_63	RPS10_BGKLV13_64
Index Well Position	S20	S21
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/D6.png	DNA_Library_LV13-14/set1/E6.png
RIN	9.3	9.2
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G2.png	RNA_Library_LV13-14-16/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-63	BGKLV13-64
RBP	RPS10	RPS10
Batch_ID	BGKLV13	BGKLV13
WB_result	33.700	36.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2162	2163

Sequencing Information

	BGKLV13-63	BGKLV13-64
Sample_ID	BGKLV13-63	BGKLV13-64
Sample Name	RPS10_BGKLV13_63	RPS10_BGKLV13_64
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	39,250,000	43,070,000
total_aligned_reads	37,133,116	40,891,046
unique_aligned_reads	34,161,054	37,480,516
percent_uniqueAligned	0.87035	0.87022
correlation_replicates	0.996541	0.996541
spikein_reads	94,636	86,328
percent_spikeins	0.00241	0.00200
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	804	805

Data Submission Information

	BGKLV13-63	BGKLV13-63
ENCODE_alias	brenton-graveley:RPS10_BGKLV13	brenton-graveley:RPS10-BGKLV13-K562
ENCODE_accession	ENCSR004RGI	ENCSR819WUX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-63	BGKLV13-63
Sample Name	RPS10_BGKLV13_63	RPS10_BGKLV13_63
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2782	6915

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
RPS10_BGKLV13_63_GTGGCC_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	804	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	13394
RPS10_BGKLV13_63_GTGGCC_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	804	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	13446
RPS10_BGKLV13_63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	804					GRCh38	V40	RPS10_BGKLV13_63_GTGGCC_L006_R1_001.fastq.gz,RPS10_BGKLV13_63_GTGGCC_L006_R2_001.fastq.gz		ENCORE2	13498
RPS10_BGKLV13_63_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	804					GRCh38	V40	RPS10_BGKLV13_63/Aligned.sortedByCoord.out.bam		ENCORE2	13550
RPS10_BGKLV13_63_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	804					GRCh38	V40	RPS10_BGKLV13_63/Aligned.sortedByCoord.out.bam		ENCORE2	13602
RPS10_BGKLV13_63_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	804					GRCh38	V40	RPS10_BGKLV13_63/Aligned.sortedByCoord.out.bam		ENCORE2	13654
RPS10_BGKLV13_63_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	804					GRCh38	V40	RPS10_BGKLV13_63/Aligned.sortedByCoord.out.bam		ENCORE2	13706
RPS10_BGKLV13_63_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	804					GRCh38	V40	RPS10_BGKLV13_63_GTGGCC_L006_R1_001.fastq.gz,RPS10_BGKLV13_63_GTGGCC_L006_R2_001.fastq.gz		ENCORE2	13758
RPS10_BGKLV13_64_GTTTCG_L006_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	805	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	13395
RPS10_BGKLV13_64_GTTTCG_L006_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	805	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	13447
RPS10_BGKLV13_64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	805					GRCh38	V40	RPS10_BGKLV13_64_GTTTCG_L006_R1_001.fastq.gz,RPS10_BGKLV13_64_GTTTCG_L006_R2_001.fastq.gz		ENCORE2	13499
RPS10_BGKLV13_64_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	805					GRCh38	V40	RPS10_BGKLV13_64/Aligned.sortedByCoord.out.bam		ENCORE2	13551
RPS10_BGKLV13_64_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	805					GRCh38	V40	RPS10_BGKLV13_64/Aligned.sortedByCoord.out.bam		ENCORE2	13603
RPS10_BGKLV13_64_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	805					GRCh38	V40	RPS10_BGKLV13_64/Aligned.sortedByCoord.out.bam		ENCORE2	13655
RPS10_BGKLV13_64_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	805					GRCh38	V40	RPS10_BGKLV13_64/Aligned.sortedByCoord.out.bam		ENCORE2	13707
RPS10_BGKLV13_64_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	805					GRCh38	V40	RPS10_BGKLV13_64_GTTTCG_L006_R1_001.fastq.gz,RPS10_BGKLV13_64_GTTTCG_L006_R2_001.fastq.gz		ENCORE2	13759