RPLP0 RNA-Seq in K562

General Information


RBP	RPLP0
Cell_Line	K562
Method	CRISPR
Exp_Name	RPLP0-BGKcLV11-K562
ENCODE_series_ID	ENCSR717MMB
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR928MEW
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	RPLP0-BGKcLV11-89
Rep2	RPLP0-BGKcLV11-90
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	11.0
Rep2_qPCR	0.0
Rep1_WB	57.3
Rep2_WB	67.6
Antibody Cat#	A302-882A
Antibody Lot#
Antibody DCC ID	ENCAB053FZB
Status	Released
Project	ENCODE4
ID	188

Experiment Information (Status: Released)

	BGKcLV11-89	BGKcLV11-90
idx	405	406
TRCN#_or_BGC#	BGC#0000020	BGC#0000020
shRNA_or_gRNA_sequence	TATCCGAAATGTTTCATTGT	TATCCGAAATGTTTCATTGT
PAM	GGG	GGG
Name	RPLP0-C2-A	RPLP0-C2-A
Sample_ID	BGKcLV11-89	BGKcLV11-90
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	RPLP0	RPLP0
qPCR_result	11.0	0.0
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3006	3049
WB_result	57.3	67.6
Ave_WB	62.4
WB_DONE_date	8/13/18
MW	34kDa
IP	1
antibody_Cat#	A302-882A
Antibody DCC ID	ENCAB053FZB
submitted_to_DCC_date	2/22/19
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4507	4508

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

	BGKcLV11-89	BGKcLV11-90
Sample_ID	BGKcLV11-89	BGKcLV11-90
Sample Name	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-90
Sample Name	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-90
RBP	RPLP0	RPLP0
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2689	2690

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-89	BGKcLV11-90
Sample #	17	18
Sample Name	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-90
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	2-A1	2-B1
Tecan	65.68	33.47
Tecan_date	2019-03-13	2019-03-13
Size_bp	301	293
Peak_Molarity	131.00	112.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/A3.png	DNA_Library_set42/set1/B3.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_set42/set1/A3.png	RNA_Library_set42/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-89	BGKcLV11-90
RBP	RPLP0	RPLP0
Batch_ID	BGKcLV11	BGKcLV11
WB_result	57.300	67.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	17	18

Sequencing Information

	BGKcLV11-89	BGKcLV11-90
Sample_ID	BGKcLV11-89	BGKcLV11-90
Sample Name	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-90
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	107,444,298	103,198,874
total_aligned_reads	105,353,226	100,084,426
unique_aligned_reads	95,269,824	90,079,772
percent_uniqueAligned	0.88669	0.87288
correlation_replicates	0.987234	0.987234
spikein_reads	93,854	89,512
percent_spikeins	0.00087	0.00087
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	63	64

Data Submission Information

	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-90	BGKcLV11-90	BGKcLV11-90	BGKcLV11-90
ENCODE_alias	brenton-graveley:RPLP0-BGKcLV11	brenton-graveley:RPLP0-BGKcLV11-89	brenton-graveley:L-RPLP0-BGKcLV11-89	brenton-graveley:RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPLP0-BGKcLV11-K562	brenton-graveley:RPLP0-BGKcLV11-90	brenton-graveley:L-RPLP0-BGKcLV11-90	brenton-graveley:RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR928MEW	ENCBS143VWQ	ENCLB187ZYT	ENCFF777ZBM	ENCFF465OMJ	ENCSR717MMB	ENCBS091DVU	ENCLB977JBP	ENCFF738EQF	ENCFF692SOK
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-89	BGKcLV11-90	BGKcLV11-90	BGKcLV11-90	BGKcLV11-90
Sample Name	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-89	RPLP0-BGKcLV11-90	RPLP0-BGKcLV11-90	RPLP0-BGKcLV11-90	RPLP0-BGKcLV11-90
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		RPLP0-BGKcLV11-89.pdf	L-RPLP0-BGKcLV11-89.pdf				RPLP0-BGKcLV11-90.pdf	L-RPLP0-BGKcLV11-90.pdf
ID	769	833	915	1013	1095	7310	834	916	1014	1096

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-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	63	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	395
RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	63	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	477
RPLP0-BGKcLV11-89_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23734
RPLP0-BGKcLV11-89_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89/Aligned.sortedByCoord.out.bam		ENCORE2	23816
RPLP0-BGKcLV11-89_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89/Aligned.sortedByCoord.out.bam		ENCORE2	23898
RPLP0-BGKcLV11-89_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89/Aligned.sortedByCoord.out.bam		ENCORE2	23980
RPLP0-BGKcLV11-89_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89/Aligned.sortedByCoord.out.bam		ENCORE2	24062
RPLP0-BGKcLV11-89_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	63					GRCh38	V40	RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPLP0-BGKcLV11-89_TAATACAG+ATATTCAC_HK3H2DSXX_S17_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24144
RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	64	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	396
RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	64	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	478
RPLP0-BGKcLV11-90_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23735
RPLP0-BGKcLV11-90_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90/Aligned.sortedByCoord.out.bam		ENCORE2	23817
RPLP0-BGKcLV11-90_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90/Aligned.sortedByCoord.out.bam		ENCORE2	23899
RPLP0-BGKcLV11-90_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90/Aligned.sortedByCoord.out.bam		ENCORE2	23981
RPLP0-BGKcLV11-90_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90/Aligned.sortedByCoord.out.bam		ENCORE2	24063
RPLP0-BGKcLV11-90_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	64					GRCh38	V40	RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R1_001.filtered.trimmed.paired.fastq.gz,RPLP0-BGKcLV11-90_CGGCGTGA+GCGCCTGT_HK3H2DSXX_S18_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24145