RPL23A RNA-Seq in K562

General Information


RBP	RPL23A
Cell_Line	K562
Method	CRISPR
Exp_Name	RPL23A-BGKcLV08-K562
ENCODE_series_ID	ENCSR004IBC
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR997ACY
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	RPL23A-BGKcLV08-59
Rep2	RPL23A-BGKcLV08-60
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	40.8
Rep2_qPCR	39.7
Rep1_WB	44.1
Rep2_WB	47.7
Antibody Cat#	A303-932A
Antibody Lot#	A303-932A
Antibody DCC ID	ENCAB435MHD
Status	Released
Project	ENCODE4
ID	209

Experiment Information (Status: Released)

	BGKcLV08-59	BGKcLV08-60
idx	284	285
TRCN#_or_BGC#	BGC#0000139	BGC#0000139
shRNA_or_gRNA_sequence	GCGCCGAAAGCGAAGAAGGA	GCGCCGAAAGCGAAGAAGGA
PAM	AGG	AGG
Name	RPL23A-75F	RPL23A-75F
Sample_ID	BGKcLV08-59	BGKcLV08-60
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	RPL23A	RPL23A
qPCR_result	40.8	39.7
Ave_qPCR	40.3
RT-qPCR_primer-F	aagccaacaagcaccagatt
RT-qPCR_primer-R	atcaggagccagtcgaacat
protein_conc	3280	3436
WB_result	44.1	47.7
Ave_WB	45.9
WB_DONE_date	3/23/18
MW	18kDa
IP	1	1
antibody_Cat#	A303-932A	A303-932A
Antibody DCC ID	ENCAB435MHD
submitted_to_DCC_date	9/6/18
Rep1_TPM	194	0
Rep2_TPM	337.8	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4384	4385

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPL23A	Product_ID: A303-932A Lot_ID: 1 Source: Bethyl Labs Target Name: RPL23A-human

Experiment Status

	BGKcLV08-59	BGKcLV08-60
Sample_ID	BGKcLV08-59	BGKcLV08-60
Sample Name
Sample Name	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-60
RBP	RPL23A	RPL23A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6189	6190

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-59	BGKcLV08-60
Sample #	25	26
Sample Name	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-60
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	288	283
Peak_Molarity	48.00	54.80
libSampleQC_DNA_Well	DNA_Library_set41/set2/A4.png	DNA_Library_set41/set2/B4.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set41/set2/E11.png	RNA_Library_set41/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-59	BGKcLV08-60
RBP	RPL23A	RPL23A
Batch_ID	BGKcLV08	BGKcLV08
WB_result	44.100	47.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	875	876

Sequencing Information

	BGKcLV08-59	BGKcLV08-60
Sample_ID	BGKcLV08-59	BGKcLV08-60
Sample Name	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-60
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	167,393,116	110,099,162
total_aligned_reads	165,133,002	105,489,562
unique_aligned_reads	147,939,328	94,270,398
percent_uniqueAligned	0.88378	0.85623
correlation_replicates	0.988847	0.988847
spikein_reads	287,230	140,782
percent_spikeins	0.00172	0.00128
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	281	282

Data Submission Information

	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-60	BGKcLV08-60	BGKcLV08-60	BGKcLV08-60
ENCODE_alias	brenton-graveley:RPL23A-BGKcLV08	brenton-graveley:RPL23A-BGKcLV08-59	brenton-graveley:L-RPL23A-BGKcLV08-59	brenton-graveley:RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGKcLV08-K562	brenton-graveley:RPL23A-BGKcLV08-60	brenton-graveley:L-RPL23A-BGKcLV08-60	brenton-graveley:RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR997ACY	ENCBS759JGW	ENCLB524MAE	ENCFF431CQQ	ENCFF977VFJ	ENCSR004IBC	ENCBS693ASC	ENCLB949RDH	ENCFF761WDJ	ENCFF058KOZ
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	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-59	BGKcLV08-60	BGKcLV08-60	BGKcLV08-60	BGKcLV08-60
Sample Name	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-59	RPL23A-BGKcLV08-60	RPL23A-BGKcLV08-60	RPL23A-BGKcLV08-60	RPL23A-BGKcLV08-60
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		RPL23A-BGKcLV08-59.pdf	L-RPL23A-BGKcLV08-59.pdf				RPL23A-BGKcLV08-60.pdf	L-RPL23A-BGKcLV08-60.pdf
ID	1139	1198	1268	1338	1402	7307	1199	1269	1339	1403

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	281				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	545
RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	281				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	615
RPL23A-BGKcLV08-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26783
RPL23A-BGKcLV08-59_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	26853
RPL23A-BGKcLV08-59_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	26923
RPL23A-BGKcLV08-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	26993
RPL23A-BGKcLV08-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59/Aligned.sortedByCoord.out.bam		ENCORE2	27063
RPL23A-BGKcLV08-59_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	281	GRCh38	V40	RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGKcLV08-59_ACTAAGAT+AACCGCGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27133
RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	282				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	546
RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	282				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	616
RPL23A-BGKcLV08-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26784
RPL23A-BGKcLV08-60_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	26854
RPL23A-BGKcLV08-60_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	26924
RPL23A-BGKcLV08-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	26994
RPL23A-BGKcLV08-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60/Aligned.sortedByCoord.out.bam		ENCORE2	27064
RPL23A-BGKcLV08-60_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	282	GRCh38	V40	RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGKcLV08-60_GTCGGAGC+GGTTATAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27134