RPL23A RNA-Seq in HepG2

General Information


RBP	RPL23A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPL23A-BGHcLV09-HepG2
ENCODE_series_ID	ENCSR780BLP
Batch_ID	BGHcLV09
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR925OFV
ENCODE_CN_Exp_ID	ENCSR300EBW
Rep1	RPL23A-BGHcLV09-11
Rep2	RPL23A-BGHcLV09-12
CN1	NT-BGHcLV09-1
CN2	NT-BGHcLV09-2
Rep1_qPCR	79.0
Rep2_qPCR	78.4
Rep1_WB	53.9
Rep2_WB	58.0
Antibody Cat#	A303-932A
Antibody Lot#
Antibody DCC ID	ENCAB435MHD
Status	Released
Project	ENCODE4
ID	217

Experiment Information (Status: Released)

	BGHcLV09-11	BGHcLV09-12
idx	173	174
TRCN#_or_BGC#	BGC#0000139	BGC#0000139
shRNA_or_gRNA_sequence	GCGCCGAAAGCGAAGAAGGA	GCGCCGAAAGCGAAGAAGGA
PAM	AGG	AGG
Name	RPL23A-75F	RPL23A-75F
Sample_ID	BGHcLV09-11	BGHcLV09-12
transduction_Date	4/20/18	4/20/18
days	D6	D6
RBP_name	RPL23A	RPL23A
qPCR_result	79.0	78.4
Ave_qPCR	78.7
RT-qPCR_primer-F	aagccaacaagcaccagatt
RT-qPCR_primer-R	atcaggagccagtcgaacat
protein_conc	2469	3152
WB_result	53.9	58.0
Ave_WB	55.9
WB_DONE_date	5/1/18
MW	18kDa
IP	1
antibody_Cat#	A303-932A
Antibody DCC ID	ENCAB435MHD
submitted_to_DCC_date	9/6/18
Rep1_TPM	1735	0
Rep2_TPM	1553	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6316	6317

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

	BGHcLV09-11	BGHcLV09-12
Sample_ID	BGHcLV09-11	BGHcLV09-12
Sample Name
Sample Name	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-12
RBP	RPL23A	RPL23A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6261	6262

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV09-11	BGHcLV09-12
Sample #	43	44
Sample Name	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-12
Sample_Name_Alias
Index Well Position	G06	H06
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	267	267
Peak_Molarity	38.70	31.40
libSampleQC_DNA_Well	DNA_Library_set41/set5/G6.png	DNA_Library_set41/set5/H6.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set41/set1/C6.png	RNA_Library_set41/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV09-11	BGHcLV09-12
RBP	RPL23A	RPL23A
Batch_ID	BGHcLV09	BGHcLV09
WB_result	53.900	58.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	893	894

Sequencing Information

	BGHcLV09-11	BGHcLV09-12
Sample_ID	BGHcLV09-11	BGHcLV09-12
Sample Name	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-12
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	111,097,126	99,746,308
total_aligned_reads	109,028,650	97,894,608
unique_aligned_reads	101,117,002	90,573,688
percent_uniqueAligned	0.91017	0.90804
correlation_replicates	0.990212	0.990212
spikein_reads	93,410	61,978
percent_spikeins	0.00084	0.00062
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	299	300

Data Submission Information

	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-12	BGHcLV09-12	BGHcLV09-12	BGHcLV09-12
ENCODE_alias	brenton-graveley:RPL23A-BGHcLV09	brenton-graveley:RPL23A-BGHcLV09-11	brenton-graveley:L-RPL23A-BGHcLV09-11	brenton-graveley:RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGHcLV09-HepG2	brenton-graveley:RPL23A-BGHcLV09-12	brenton-graveley:L-RPL23A-BGHcLV09-12	brenton-graveley:RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR925OFV	ENCBS145YHJ	ENCLB715PIE	ENCFF602CTL	ENCFF275HJH	ENCSR780BLP	ENCBS219EXC	ENCLB012PTS	ENCFF627HYR	ENCFF165LJE
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	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-11	BGHcLV09-12	BGHcLV09-12	BGHcLV09-12	BGHcLV09-12
Sample Name	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-11	RPL23A-BGHcLV09-12	RPL23A-BGHcLV09-12	RPL23A-BGHcLV09-12	RPL23A-BGHcLV09-12
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-BGHcLV09-11.pdf	L-RPL23A-BGHcLV09-11.pdf				RPL23A-BGHcLV09-12.pdf	L-RPL23A-BGHcLV09-12.pdf
ID	1138	1196	1266	1336	1400	7306	1197	1267	1337	1401

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-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	299				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	543
RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	299				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	613
RPL23A-BGHcLV09-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	299	GRCh38	V40	RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26781
RPL23A-BGHcLV09-11_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	299	GRCh38	V40	RPL23A-BGHcLV09-11/Aligned.sortedByCoord.out.bam		ENCORE2	26851
RPL23A-BGHcLV09-11_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	299	GRCh38	V40	RPL23A-BGHcLV09-11/Aligned.sortedByCoord.out.bam		ENCORE2	26921
RPL23A-BGHcLV09-11_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	299	GRCh38	V40	RPL23A-BGHcLV09-11/Aligned.sortedByCoord.out.bam		ENCORE2	26991
RPL23A-BGHcLV09-11_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	299	GRCh38	V40	RPL23A-BGHcLV09-11/Aligned.sortedByCoord.out.bam		ENCORE2	27061
RPL23A-BGHcLV09-11_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	299	GRCh38	V40	RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGHcLV09-11_GTTCCAAT+AATTCTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27131
RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	300				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	544
RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	300				NT-BGHcLV09-1_ATATGGAT+CTGTATTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV09-2_GCGCAAGC+TCACGCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	614
RPL23A-BGHcLV09-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	300	GRCh38	V40	RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26782
RPL23A-BGHcLV09-12_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	300	GRCh38	V40	RPL23A-BGHcLV09-12/Aligned.sortedByCoord.out.bam		ENCORE2	26852
RPL23A-BGHcLV09-12_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	300	GRCh38	V40	RPL23A-BGHcLV09-12/Aligned.sortedByCoord.out.bam		ENCORE2	26922
RPL23A-BGHcLV09-12_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	300	GRCh38	V40	RPL23A-BGHcLV09-12/Aligned.sortedByCoord.out.bam		ENCORE2	26992
RPL23A-BGHcLV09-12_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	300	GRCh38	V40	RPL23A-BGHcLV09-12/Aligned.sortedByCoord.out.bam		ENCORE2	27062
RPL23A-BGHcLV09-12_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	300	GRCh38	V40	RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPL23A-BGHcLV09-12_ACCTTGGC+GGCCTCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27132