RPLP0 RNA-Seq in HepG2

General Information


RBP	RPLP0
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPLP0-BGHcLV03-HepG2
ENCODE_series_ID	ENCSR890HZD
Batch_ID	BGHcLV03
Pool ID	Pool-160201
Local_Set_Name	BGHcLV03
ENCODE_KD_Exp_ID	ENCSR000SKS
ENCODE_CN_Exp_ID	ENCSR105NML
Rep1	RPLP0_BGHcLV03-17
Rep2	RPLP0_BGHcLV03-18
CN1	NT_BGHcLV03-1
CN2	NT_BGHcLV03-2
Rep1_qPCR	95.5
Rep2_qPCR	95.5
Rep1_WB	57.4
Rep2_WB	41.4
Antibody Cat#	A302-882A
Antibody Lot#	A302-882A
Antibody DCC ID	ENCAB053FZB
Status	Released
Project	ENCODE3
ID	576

Experiment Information (Status: Released)

	BGHcLV03-17	BGHcLV03-18
idx	17	18
TRCN#_or_BGC#	BGC#0000020	BGC#0000020
shRNA_or_gRNA_sequence	TATCCGAAATGTTTCATTGT	TATCCGAAATGTTTCATTGT
PAM
Name	RPLP0-C2-A	RPLP0-C2-A
Sample_ID	BGHcLV03-17	BGHcLV03-18
transduction_Date	12/16/2015	12/16/2015
days	D6	D6
RBP_name	RPLP0	RPLP0
qPCR_result	95.5	95.5
Ave_qPCR	95.5
RT-qPCR_primer-F	gcgacctggaagtccaacta
RT-qPCR_primer-R	tgtctgctcccacaatgaaa
protein_conc	1593	1257
WB_result	57.4	41.4
Ave_WB	49.4
WB_DONE_date	1/4/2016
MW	34kDa
IP	1
antibody_Cat#	A302-882A	A302-882A
Antibody DCC ID	ENCAB053FZB	ENCAB053FZB
submitted_to_DCC_date	9/28/16
Rep1_TPM	643	0
Rep2_TPM	681	0
Action	Ready	Ready
Library_start_date	1/8/2016	1/8/2016
repeat_library
Note
ID	6158	6159

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

	BGHcLV03-17	BGHcLV03-18
Sample_ID	BGHcLV03-17	BGHcLV03-18
Sample Name	RPLP0_BGHcLV03-17	RPLP0_BGHcLV03-18
Sample Name	RPLP0_BGHcLV03-17	RPLP0_BGHcLV03-18
RBP	RPLP0	RPLP0
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-09	2016-03-09
Project	ENCODE3	ENCODE3
Note
ID	1105	1106

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV03-17	BGHcLV03-18
Sample #
Sample Name	RPLP0-BGHcLV03-17	RPLP0-BGHcLV03-18
Sample_Name_Alias	RPLP0_BGHcLV03-17	RPLP0_BGHcLV03-18
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-01-08	2016-01-08
Lib_ID	Lib-160108	Lib-160108
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_cLV02/set1/A3.png	DNA_Library_cLV02/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_cLV02/set1/C4.png	RNA_Library_cLV02/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV03-17	BGHcLV03-18
RBP	RPLP0	RPLP0
Batch_ID	BGHcLV03	BGHcLV03
WB_result	57.400	41.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2802	2803

Sequencing Information

	BGHcLV03-17	BGHcLV03-18
Sample_ID	BGHcLV03-17	BGHcLV03-18
Sample Name	RPLP0_BGHcLV03-17	RPLP0_BGHcLV03-18
Pool ID	Pool-160201	Pool-160201
LocalServer_folder	BGHcLV03	BGHcLV03
total_reads	54,964,002	63,711,114
total_aligned_reads	48,409,694	56,615,446
unique_aligned_reads	45,439,892	53,071,022
percent_uniqueAligned	0.82672	0.83299
correlation_replicates	0.993624	0.993624
spikein_reads	108,012	101,926
percent_spikeins	0.00197	0.00160
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1451	1452

Data Submission Information

	BGHcLV03-17	BGHcLV03-17
ENCODE_alias	brenton-graveley:RPLP0_BGHcLV03	brenton-graveley:RPLP0-BGHcLV03-HepG2
ENCODE_accession	ENCSR000SKS	ENCSR890HZD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV03-17	BGHcLV03-17
Sample Name	RPLP0_BGHcLV03-17	RPLP0_BGHcLV03-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3114	6912

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_BGHcLV03-17_GATCAG_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1451	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22924
RPLP0_BGHcLV03-17_GATCAG_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1451	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22942
RPLP0_BGHcLV03-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17_GATCAG_L006_001.R1.fastq.gz,RPLP0_BGHcLV03-17_GATCAG_L006_001.R2.fastq.gz		ENCORE2	22960
RPLP0_BGHcLV03-17_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	22978
RPLP0_BGHcLV03-17_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	22996
RPLP0_BGHcLV03-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	23014
RPLP0_BGHcLV03-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17/Aligned.sortedByCoord.out.bam		ENCORE2	23032
RPLP0_BGHcLV03-17_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1451					GRCh38	V40	RPLP0_BGHcLV03-17_GATCAG_L006_001.R1.fastq.gz,RPLP0_BGHcLV03-17_GATCAG_L006_001.R2.fastq.gz		ENCORE2	23050
RPLP0_BGHcLV03-18_TAGCTT_L006_001.R1.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1452	HiSeq2500	100	paired-ended	1				NT_BGHcLV03-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22925
RPLP0_BGHcLV03-18_TAGCTT_L006_001.R2.fastq.gz	ENCODE_DATA/BGHcLV03/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1452	HiSeq2500	100	paired-ended	2				NT_BGHcLV03-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHcLV03-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22943
RPLP0_BGHcLV03-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18_TAGCTT_L006_001.R1.fastq.gz,RPLP0_BGHcLV03-18_TAGCTT_L006_001.R2.fastq.gz		ENCORE2	22961
RPLP0_BGHcLV03-18_Signal.Unique.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	22979
RPLP0_BGHcLV03-18_Signal.Unique.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	22997
RPLP0_BGHcLV03-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	23015
RPLP0_BGHcLV03-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGHcLV03/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18/Aligned.sortedByCoord.out.bam		ENCORE2	23033
RPLP0_BGHcLV03-18_quant.sf	ENCODE_DATA/BGHcLV03/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1452					GRCh38	V40	RPLP0_BGHcLV03-18_TAGCTT_L006_001.R1.fastq.gz,RPLP0_BGHcLV03-18_TAGCTT_L006_001.R2.fastq.gz		ENCORE2	23051