RPLP0 RNA-Seq in HepG2

General Information


RBP	RPLP0
Cell_Line	HepG2
Method	shRNA
Exp_Name	RPLP0-BGHLV18-HepG2
ENCODE_series_ID	ENCSR808WDS
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR082YGI
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	RPLP0_BGHLV18_53
Rep2	RPLP0_BGHLV18_54
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	81.4
Rep2_qPCR	73.1
Rep1_WB	37.5
Rep2_WB	47.6
Antibody Cat#	A302-882A
Antibody Lot#	A302-882A
Antibody DCC ID	ENCAB053FZB
Status	Archived
Project	ENCODE3
ID	459

Experiment Information (Status: Released)

	BGHLV18-53	BGHLV18-54
idx	353	354
TRCN#_or_BGC#	TRCN0000117527	TRCN0000117527
shRNA_or_gRNA_sequence	GCTTTAGGTATCACCACTAAA	GCTTTAGGTATCACCACTAAA
PAM
Name	RPLP0	RPLP0
Sample_ID	BGHLV18-53	BGHLV18-54
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	RPLP0	RPLP0
qPCR_result	81.4	73.1
Ave_qPCR	77.2
RT-qPCR_primer-F	cctcactgagatcagggacat
RT-qPCR_primer-R	gtgacttcacatggggcaat
protein_conc	3040	2757
WB_result	37.5	47.6
Ave_WB	42.6
WB_DONE_date	2/9/2015
MW	34kDa
IP	1	1
antibody_Cat#	A302-882A	A302-882A
Antibody DCC ID	ENCAB053FZB	ENCAB053FZB
submitted_to_DCC_date	10/26/2016
Rep1_TPM	643.4	0
Rep2_TPM	681.1	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2418	2419

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPLP0	Product_ID: A302-882A Lot_ID: 1 Source: Bethyl Labs Target Name: RPLP0-human

Experiment Status

	BGHLV18-53	BGHLV18-54
Sample_ID	BGHLV18-53	BGHLV18-54
Sample Name	RPLP0_BGHLV18_53	RPLP0_BGHLV18_54
Sample Name	RPLP0_BGHLV18_53	RPLP0_BGHLV18_54
RBP	RPLP0	RPLP0
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	648	649

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-53	BGHLV18-54
Sample #
Sample Name	RPLP0-BGHLV18-53	RPLP0-BGHLV18-54
Sample_Name_Alias	RPLP0_BGHLV18_53	RPLP0_BGHLV18_54
Index Well Position	S09	S10
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/A5.png	DNA_Library_LV18-19/set1/B5.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV18-19/set1/G11.png	RNA_Library_LV18-19/set1/H11.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-53	BGHLV18-54
RBP	RPLP0	RPLP0
Batch_ID	BGHLV18	BGHLV18
WB_result	37.500	47.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2332	2333

Sequencing Information

	BGHLV18-53	BGHLV18-54
Sample_ID	BGHLV18-53	BGHLV18-54
Sample Name	RPLP0_BGHLV18_53	RPLP0_BGHLV18_54
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	50,640,000	52,670,000
total_aligned_reads	46,131,800	47,820,952
unique_aligned_reads	43,464,714	45,037,682
percent_uniqueAligned	0.85831	0.85509
correlation_replicates	0.999588	0.999588
spikein_reads	160,180	145,664
percent_spikeins	0.00316	0.00277
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	974	975

Data Submission Information

	BGHLV18-53	BGHLV18-53
ENCODE_alias	brenton-graveley:RPLP0_BGHLV18	brenton-graveley:RPLP0-BGHLV18-HepG2
ENCODE_accession	ENCSR082YGI	ENCSR808WDS
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-53	BGHLV18-53
Sample Name	RPLP0_BGHLV18_53	RPLP0_BGHLV18_53
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2841	6913

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
RPLP0_BGHLV18_53_GATCAG_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	974	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14822
RPLP0_BGHLV18_53_GATCAG_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	974	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14860
RPLP0_BGHLV18_53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	974					GRCh38	V40	RPLP0_BGHLV18_53_GATCAG_L005_R1_001.fastq.gz,RPLP0_BGHLV18_53_GATCAG_L005_R2_001.fastq.gz		ENCORE2	14898
RPLP0_BGHLV18_53_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	974					GRCh38	V40	RPLP0_BGHLV18_53/Aligned.sortedByCoord.out.bam		ENCORE2	14936
RPLP0_BGHLV18_53_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	974					GRCh38	V40	RPLP0_BGHLV18_53/Aligned.sortedByCoord.out.bam		ENCORE2	14974
RPLP0_BGHLV18_53_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	974					GRCh38	V40	RPLP0_BGHLV18_53/Aligned.sortedByCoord.out.bam		ENCORE2	15012
RPLP0_BGHLV18_53_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	974					GRCh38	V40	RPLP0_BGHLV18_53/Aligned.sortedByCoord.out.bam		ENCORE2	15050
RPLP0_BGHLV18_53_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	974					GRCh38	V40	RPLP0_BGHLV18_53_GATCAG_L005_R1_001.fastq.gz,RPLP0_BGHLV18_53_GATCAG_L005_R2_001.fastq.gz		ENCORE2	15088
RPLP0_BGHLV18_54_TAGCTT_L005_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	975	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14823
RPLP0_BGHLV18_54_TAGCTT_L005_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	975	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14861
RPLP0_BGHLV18_54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	975					GRCh38	V40	RPLP0_BGHLV18_54_TAGCTT_L005_R1_001.fastq.gz,RPLP0_BGHLV18_54_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	14899
RPLP0_BGHLV18_54_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	975					GRCh38	V40	RPLP0_BGHLV18_54/Aligned.sortedByCoord.out.bam		ENCORE2	14937
RPLP0_BGHLV18_54_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	975					GRCh38	V40	RPLP0_BGHLV18_54/Aligned.sortedByCoord.out.bam		ENCORE2	14975
RPLP0_BGHLV18_54_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	975					GRCh38	V40	RPLP0_BGHLV18_54/Aligned.sortedByCoord.out.bam		ENCORE2	15013
RPLP0_BGHLV18_54_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	975					GRCh38	V40	RPLP0_BGHLV18_54/Aligned.sortedByCoord.out.bam		ENCORE2	15051
RPLP0_BGHLV18_54_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	975					GRCh38	V40	RPLP0_BGHLV18_54_TAGCTT_L005_R1_001.fastq.gz,RPLP0_BGHLV18_54_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	15089