RPS2 RNA-Seq in HepG2

General Information


RBP	RPS2
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPS2-BGHLV18-HepG2
ENCODE_series_ID	ENCSR188XBQ
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR667RIA
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RPS2_BGHLV18_55
Rep2	RPS2_BGHLV18_56
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	75.2
Rep2_qPCR	72.4
Rep1_WB	72.5
Rep2_WB	52.7
Antibody Cat#	A303-209A
Antibody Lot#	A303-209A
Antibody DCC ID	ENCAB353OXX
Status	Released
Project	ENCODE3
ID	460

Experiment Information (Status: Released)

	BGHLV18-55	BGHLV18-56
idx	355	356
TRCN#_or_BGC#	TRCN0000117482	TRCN0000117482
shRNA_or_gRNA_sequence	CCACCTTTGATGCCATTTCTA	CCACCTTTGATGCCATTTCTA
PAM
Name	RPS2	RPS2
Sample_ID	BGHLV18-55	BGHLV18-56
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RPS2	RPS2
qPCR_result	75.2	72.4
Ave_qPCR	73.8
RT-qPCR_primer-F	tgctcatgatggctggtatc
RT-qPCR_primer-R	gggggtcaggtagctgtagg
protein_conc	3375	3235
WB_result	72.5	52.7
Ave_WB	62.6
WB_DONE_date	4/15/2015
MW	31kDa
IP	1	1
antibody_Cat#	A303-209A	A303-209A
Antibody DCC ID	ENCAB353OXX	ENCAB353OXX
submitted_to_DCC_date	5/6/2015
Rep1_TPM	151	0
Rep2_TPM	180.5	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2420	2421

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SARNP	Product_ID: A303-209A Lot_ID: 1 Source: Bethyl Labs Target Name: SARNP-human

Experiment Status

	BGHLV18-55	BGHLV18-56
Sample_ID	BGHLV18-55	BGHLV18-56
Sample Name	RPS2_BGHLV18_55	RPS2_BGHLV18_56
Sample Name	RPS2_BGHLV18_55	RPS2_BGHLV18_56
RBP	RPS2	RPS2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	650	651

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-55	BGHLV18-56
Sample #
Sample Name	RPS2-BGHLV18-55	RPS2-BGHLV18-56
Sample_Name_Alias	RPS2_BGHLV18_55	RPS2_BGHLV18_56
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C5.png	DNA_Library_LV18-19/set1/D5.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV18-19/set1/A12.png	RNA_Library_LV18-19/set1/B12.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-55	BGHLV18-56
RBP	RPS2	RPS2
Batch_ID	BGHLV18	BGHLV18
WB_result	72.500	52.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2334	2335

Sequencing Information

	BGHLV18-55	BGHLV18-56
Sample_ID	BGHLV18-55	BGHLV18-56
Sample Name	RPS2_BGHLV18_55	RPS2_BGHLV18_56
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	52,770,000	57,230,000
total_aligned_reads	47,642,692	51,434,378
unique_aligned_reads	44,984,884	48,579,856
percent_uniqueAligned	0.85247	0.84885
correlation_replicates	0.995706	0.995706
spikein_reads	191,716	123,856
percent_spikeins	0.00363	0.00216
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	976	977

Data Submission Information

	BGHLV18-55	BGHLV18-55
ENCODE_alias	brenton-graveley:RPS2_BGHLV18	brenton-graveley:RPS2-BGHLV18-HepG2
ENCODE_accession	ENCSR667RIA	ENCSR188XBQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-55	BGHLV18-55
Sample Name	RPS2_BGHLV18_55	RPS2_BGHLV18_55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2842	6918

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
RPS2_BGHLV18_55_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	976	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14824
RPS2_BGHLV18_55_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	976	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14862
RPS2_BGHLV18_55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55_GGCTAC_L005_R1_001.fastq.gz,RPS2_BGHLV18_55_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	14900
RPS2_BGHLV18_55_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55/Aligned.sortedByCoord.out.bam		ENCORE2	14938
RPS2_BGHLV18_55_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55/Aligned.sortedByCoord.out.bam		ENCORE2	14976
RPS2_BGHLV18_55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55/Aligned.sortedByCoord.out.bam		ENCORE2	15014
RPS2_BGHLV18_55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55/Aligned.sortedByCoord.out.bam		ENCORE2	15052
RPS2_BGHLV18_55_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	976					GRCh38	V40	RPS2_BGHLV18_55_GGCTAC_L005_R1_001.fastq.gz,RPS2_BGHLV18_55_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	15090
RPS2_BGHLV18_56_CTTGTA_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	977	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14825
RPS2_BGHLV18_56_CTTGTA_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	977	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14863
RPS2_BGHLV18_56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56_CTTGTA_L005_R1_001.fastq.gz,RPS2_BGHLV18_56_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	14901
RPS2_BGHLV18_56_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56/Aligned.sortedByCoord.out.bam		ENCORE2	14939
RPS2_BGHLV18_56_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56/Aligned.sortedByCoord.out.bam		ENCORE2	14977
RPS2_BGHLV18_56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56/Aligned.sortedByCoord.out.bam		ENCORE2	15015
RPS2_BGHLV18_56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56/Aligned.sortedByCoord.out.bam		ENCORE2	15053
RPS2_BGHLV18_56_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	977					GRCh38	V40	RPS2_BGHLV18_56_CTTGTA_L005_R1_001.fastq.gz,RPS2_BGHLV18_56_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	15091