RPL23A RNA-Seq in HepG2

General Information


RBP	RPL23A
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPL23A-BGHLV18-HepG2
ENCODE_series_ID	ENCSR732XCU
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR706SXN
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RPL23A_BGHLV18_51
Rep2	RPL23A_BGHLV18_52
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	58.4
Rep2_qPCR	67.2
Rep1_WB	23.4
Rep2_WB	35.8
Antibody Cat#	A303-932A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB435MHD
Status	Archived
Project	ENCODE3
ID	458

Experiment Information (Status: Released)

	BGHLV18-51	BGHLV18-52
idx	351	352
TRCN#_or_BGC#	TRCN0000075031	TRCN0000075031
shRNA_or_gRNA_sequence	CCTCCTAAAGCTGAAGCCAAA	CCTCCTAAAGCTGAAGCCAAA
PAM
Name	RPL23A	RPL23A
Sample_ID	BGHLV18-51	BGHLV18-52
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RPL23A	RPL23A
qPCR_result	58.4	67.2
Ave_qPCR	62.8
RT-qPCR_primer-F	aagccaacaagcaccagatt
RT-qPCR_primer-R	atcaggagccagtcgaacat
protein_conc	4192	4423
WB_result	23.4	35.8
Ave_WB	29.6
WB_DONE_date	1/21/2015
MW
IP	1	1
antibody_Cat#	A303-932A	A303-932A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	188.3	0
Rep2_TPM	209.5	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2416	2417

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV18-51	BGHLV18-52
Sample_ID	BGHLV18-51	BGHLV18-52
Sample Name	RPL23A_BGHLV18_51	RPL23A_BGHLV18_52
Sample Name	RPL23A_BGHLV18_51	RPL23A_BGHLV18_52
RBP	RPL23A	RPL23A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	646	647

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-51	BGHLV18-52
Sample #
Sample Name	RPL23A-BGHLV18-51	RPL23A-BGHLV18-52
Sample_Name_Alias	RPL23A_BGHLV18_51	RPL23A_BGHLV18_52
Index Well Position	S07	S08
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/G4.png	DNA_Library_LV18-19/set1/H4.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV18-19/set1/E11.png	RNA_Library_LV18-19/set1/F11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-51	BGHLV18-52
RBP	RPL23A	RPL23A
Batch_ID	BGHLV18	BGHLV18
WB_result	23.400	35.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2330	2331

Sequencing Information

	BGHLV18-51	BGHLV18-52
Sample_ID	BGHLV18-51	BGHLV18-52
Sample Name	RPL23A_BGHLV18_51	RPL23A_BGHLV18_52
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	45,280,000	61,930,000
total_aligned_reads	41,339,468	55,756,578
unique_aligned_reads	39,039,680	52,592,790
percent_uniqueAligned	0.86218	0.84923
correlation_replicates	0.989794	0.989794
spikein_reads	71,398	196,772
percent_spikeins	0.00158	0.00318
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	972	973

Data Submission Information

	BGHLV18-51	BGHLV18-51
ENCODE_alias	brenton-graveley:RPL23A_BGHLV18	brenton-graveley:RPL23A-BGHLV18-HepG2
ENCODE_accession	ENCSR706SXN	ENCSR732XCU
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-51	BGHLV18-51
Sample Name	RPL23A_BGHLV18_51	RPL23A_BGHLV18_51
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2840	6911

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
RPL23A_BGHLV18_51_CAGATC_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	972	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14820
RPL23A_BGHLV18_51_CAGATC_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	972	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14858
RPL23A_BGHLV18_51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	972					GRCh38	V40	RPL23A_BGHLV18_51_CAGATC_L004_R1_001.fastq.gz,RPL23A_BGHLV18_51_CAGATC_L004_R2_001.fastq.gz		ENCORE2	14896
RPL23A_BGHLV18_51_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	972					GRCh38	V40	RPL23A_BGHLV18_51/Aligned.sortedByCoord.out.bam		ENCORE2	14934
RPL23A_BGHLV18_51_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	972					GRCh38	V40	RPL23A_BGHLV18_51/Aligned.sortedByCoord.out.bam		ENCORE2	14972
RPL23A_BGHLV18_51_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	972					GRCh38	V40	RPL23A_BGHLV18_51/Aligned.sortedByCoord.out.bam		ENCORE2	15010
RPL23A_BGHLV18_51_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	972					GRCh38	V40	RPL23A_BGHLV18_51/Aligned.sortedByCoord.out.bam		ENCORE2	15048
RPL23A_BGHLV18_51_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	972					GRCh38	V40	RPL23A_BGHLV18_51_CAGATC_L004_R1_001.fastq.gz,RPL23A_BGHLV18_51_CAGATC_L004_R2_001.fastq.gz		ENCORE2	15086
RPL23A_BGHLV18_52_ACTTGA_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	973	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14821
RPL23A_BGHLV18_52_ACTTGA_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	973	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14859
RPL23A_BGHLV18_52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	973					GRCh38	V40	RPL23A_BGHLV18_52_ACTTGA_L005_R1_001.fastq.gz,RPL23A_BGHLV18_52_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	14897
RPL23A_BGHLV18_52_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	973					GRCh38	V40	RPL23A_BGHLV18_52/Aligned.sortedByCoord.out.bam		ENCORE2	14935
RPL23A_BGHLV18_52_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	973					GRCh38	V40	RPL23A_BGHLV18_52/Aligned.sortedByCoord.out.bam		ENCORE2	14973
RPL23A_BGHLV18_52_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	973					GRCh38	V40	RPL23A_BGHLV18_52/Aligned.sortedByCoord.out.bam		ENCORE2	15011
RPL23A_BGHLV18_52_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	973					GRCh38	V40	RPL23A_BGHLV18_52/Aligned.sortedByCoord.out.bam		ENCORE2	15049
RPL23A_BGHLV18_52_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	973					GRCh38	V40	RPL23A_BGHLV18_52_ACTTGA_L005_R1_001.fastq.gz,RPL23A_BGHLV18_52_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	15087