RPS3A RNA-Seq in HepG2

General Information


RBP	RPS3A
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPS3A-BGHLV22-HepG2
ENCODE_series_ID	ENCSR078ZFS
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR118VQR
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	RPS3A-BGHLV22-43
Rep2	RPS3A-BGHLV22-44
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	73.5
Rep2_qPCR	80.8
Rep1_WB	52.8
Rep2_WB	49.3
Antibody Cat#	GTX105020
Antibody Lot#	GTX105020
Antibody DCC ID	ENCAB550TJZ
Status	Released
Project	ENCODE3
ID	527

Experiment Information (Status: Released)

	BGHLV22-43	BGHLV22-43	BGHLV22-44	BGHLV22-44
idx	471	471	472	472
TRCN#_or_BGC#	TRCN0000074709	TRCN0000074709	TRCN0000074709	TRCN0000074709
shRNA_or_gRNA_sequence	CCGGAAGAAGATGATGGAAAT	CCGGAAGAAGATGATGGAAAT	CCGGAAGAAGATGATGGAAAT	CCGGAAGAAGATGATGGAAAT
PAM
Name	RPS3A	RPS3A	RPS3A	RPS3A
Sample_ID	BGHLV22-43	BGHLV22-43	BGHLV22-44	BGHLV22-44
transduction_Date	10/16/2014	10/16/2014	10/16/2014	10/16/2014
days
RBP_name	RPS3A	RPS3A	RPS3A	RPS3A
qPCR_result	73.5	73.5	80.8	80.8
Ave_qPCR	77.2	77.2
RT-qPCR_primer-F	caaaaagggagccaagaaga	caaaaagggagccaagaaga
RT-qPCR_primer-R	gtgacgagcgtctttccaat	gtgacgagcgtctttccaat
protein_conc	4883	4883	4458	4458
WB_result	52.8	no change	49.3
Ave_WB	51.1
WB_DONE_date	5/4/2015	4/20/22,4/27/22
MW	30kDa	30kDa
IP	1		1
antibody_Cat#	GTX105020	A305-001A	GTX105020	lot#1
Antibody DCC ID	ENCAB550TJZ		ENCAB550TJZ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	371.7	0	0	0
Rep2_TPM	414.9	0	0	0
Action
Library_start_date	6/5/2015		6/5/2015
repeat_library
Note
ID	2540	2542	2541	2543

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

	BGHLV22-43	BGHLV22-44
Sample_ID	BGHLV22-43	BGHLV22-44
Sample Name	RPS3A-BGHLV22-43	RPS3A-BGHLV22-44
Sample Name	RPS3A-BGHLV22-43	RPS3A-BGHLV22-44
RBP	RPS3A	RPS3A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	804	805

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-43	BGHLV22-44
Sample #
Sample Name	RPS3A-BGHLV22-43	RPS3A-BGHLV22-44
Sample_Name_Alias	RPS3A-BGHLV22-43	RPS3A-BGHLV22-44
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/C9.png	DNA_Library_LV20-22-23/set1/D9.png
RIN	9.1	9.6
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/C3.png	RNA_Library_LV22-23-25/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-43	BGHLV22-44
RBP	RPS3A	RPS3A
Batch_ID	BGHLV22	BGHLV22
WB_result	52.800	49.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2490	2491

Sequencing Information

	BGHLV22-43	BGHLV22-44
Sample_ID	BGHLV22-43	BGHLV22-44
Sample Name	RPS3A-BGHLV22-43	RPS3A-BGHLV22-44
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	59,790,000	59,420,000
total_aligned_reads	54,799,676	55,054,950
unique_aligned_reads	51,684,926	51,944,038
percent_uniqueAligned	0.86444	0.87418
correlation_replicates	0.999649	0.999649
spikein_reads	264,224	247,580
percent_spikeins	0.00442	0.00417
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1112	1113

Data Submission Information

	BGHLV22-43	BGHLV22-43
ENCODE_alias	brenton-graveley:RPS3A-BGHLV22	brenton-graveley:RPS3A-BGHLV22-HepG2
ENCODE_accession	ENCSR118VQR	ENCSR078ZFS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-43	BGHLV22-43
Sample Name	RPS3A-BGHLV22-43	RPS3A-BGHLV22-43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2934	6920

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-BGHLV22-43_TTAGGC_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1112	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16302
RPS3A-BGHLV22-43_TTAGGC_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1112	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16342
RPS3A-BGHLV22-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43_TTAGGC_L002_R1_001.fastq.gz,RPS3A-BGHLV22-43_TTAGGC_L002_R2_001.fastq.gz		ENCORE2	16440
RPS3A-BGHLV22-43_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43/Aligned.sortedByCoord.out.bam		ENCORE2	16480
RPS3A-BGHLV22-43_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43/Aligned.sortedByCoord.out.bam		ENCORE2	16520
RPS3A-BGHLV22-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43/Aligned.sortedByCoord.out.bam		ENCORE2	16560
RPS3A-BGHLV22-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43/Aligned.sortedByCoord.out.bam		ENCORE2	16600
RPS3A-BGHLV22-43_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1112					GRCh38	V40	RPS3A-BGHLV22-43_TTAGGC_L002_R1_001.fastq.gz,RPS3A-BGHLV22-43_TTAGGC_L002_R2_001.fastq.gz		ENCORE2	16640
RPS3A-BGHLV22-44_TGACCA_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1113	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16303
RPS3A-BGHLV22-44_TGACCA_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1113	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16343
RPS3A-BGHLV22-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44_TGACCA_L002_R1_001.fastq.gz,RPS3A-BGHLV22-44_TGACCA_L002_R2_001.fastq.gz		ENCORE2	16441
RPS3A-BGHLV22-44_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44/Aligned.sortedByCoord.out.bam		ENCORE2	16481
RPS3A-BGHLV22-44_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44/Aligned.sortedByCoord.out.bam		ENCORE2	16521
RPS3A-BGHLV22-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44/Aligned.sortedByCoord.out.bam		ENCORE2	16561
RPS3A-BGHLV22-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44/Aligned.sortedByCoord.out.bam		ENCORE2	16601
RPS3A-BGHLV22-44_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1113					GRCh38	V40	RPS3A-BGHLV22-44_TGACCA_L002_R1_001.fastq.gz,RPS3A-BGHLV22-44_TGACCA_L002_R2_001.fastq.gz		ENCORE2	16641