RPS15A RNA-Seq in HepG2

General Information


RBP	RPS15A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS15A-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR832MUA
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR119RXN
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RPS15A-BGHcLV32-65
Rep2	RPS15A-BGHcLV32-66
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	25.5
Rep2_qPCR	49.8
Rep1_WB	64.9
Rep2_WB	69.5
Antibody Cat#	A304-990A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB489CNK
Status	Submitted
Project	ENCODE4
ID	939

Experiment Information (Status: Released)

	BGHcLV32-65	BGHcLV32-66
idx	1066	1067
TRCN#_or_BGC#	BGC#0000814	BGC#0000814
shRNA_or_gRNA_sequence	ACTTACCCAAACTGGCGGGA	ACTTACCCAAACTGGCGGGA
PAM	TGG	TGG
Name	RPS15A-90	RPS15A-90
Sample_ID	BGHcLV32-65	BGHcLV32-66
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RPS15A	RPS15A
qPCR_result	25.5	49.8
Ave_qPCR	37.7
RT-qPCR_primer-F	tggcgaatttgaaatcattg
RT-qPCR_primer-R	ttctgccatttttccaggtc
protein_conc	3423	3170
WB_result	64.9	69.5
Ave_WB	67.2
WB_DONE_date	12/7/21
MW	15KD
IP
antibody_Cat#	A304-990A	LOT #1
Antibody DCC ID	ENCAB489CNK	8/4/22
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	7245	7246

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS15A	Product_ID: A304-990A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS15A-human

Experiment Status

	BGHcLV32-65	BGHcLV32-66
Sample_ID	BGHcLV32-65	BGHcLV32-66
Sample Name
Sample Name	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-66
RBP	RPS15A	RPS15A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10377	10378

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-65	BGHcLV32-66
Sample #	51	52
Sample Name	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-66
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	292	304
Peak_Molarity	83.20	62.70
libSampleQC_DNA_Well	DNA_Library_set52/set2/C7.png	DNA_Library_set52/set2/D7.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set52/set2/G9.png	RNA_Library_set52/set2/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-65	BGHcLV32-66
RBP	RPS15A	RPS15A
Batch_ID	BGHcLV32	BGHcLV32
WB_result	64.900	69.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3228	3229

Sequencing Information

	BGHcLV32-65	BGHcLV32-66
Sample_ID	BGHcLV32-65	BGHcLV32-66
Sample Name	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-66
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	137,247,226	109,746,984
total_aligned_reads	116,774,694	97,002,714
unique_aligned_reads	109,778,754	91,532,110
percent_uniqueAligned	0.79986	0.83403
correlation_replicates	0.990065	0.990065
spikein_reads	4,938	2,340
percent_spikeins	0.00004	0.00002
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2023	2024

Data Submission Information

	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-66	BGHcLV32-66	BGHcLV32-66	BGHcLV32-66
ENCODE_alias	brenton-graveley:RPS15A-BGHcLV32	brenton-graveley:RPS15A-BGHcLV32-65	brenton-graveley:L-RPS15A-BGHcLV32-65	brenton-graveley:RPS15A-BGHcLV32-65_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGHcLV32-65_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGHcLV32-HepG2	brenton-graveley:RPS15A-BGHcLV32-66	brenton-graveley:L-RPS15A-BGHcLV32-66	brenton-graveley:RPS15A-BGHcLV32-66_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPS15A-BGHcLV32-66_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR119RXN	ENCBS724WJD	ENCLB243EBA	ENCFF083BDP	ENCFF055CVK	ENCSR832MUA	ENCBS632MXM	ENCLB683GOT	ENCFF451PTG	ENCFF534NUM
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	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-65	BGHcLV32-66	BGHcLV32-66	BGHcLV32-66	BGHcLV32-66
Sample Name	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-65	RPS15A-BGHcLV32-66	RPS15A-BGHcLV32-66	RPS15A-BGHcLV32-66	RPS15A-BGHcLV32-66
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RPS15A-BGHcLV32-65.pdf	L-RPS15A-BGHcLV32-65.pdf				RPS15A-BGHcLV32-66.pdf	L-RPS15A-BGHcLV32-66.pdf
ID	7468	7543	7655	7765	7875	7959	7544	7656	7766	7876

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
RPS15A-BGHcLV32-65_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2023	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6523
RPS15A-BGHcLV32-65_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2023	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6577
RPS15A-BGHcLV32-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGHcLV32-65_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18444
RPS15A-BGHcLV32-65_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65/Aligned.sortedByCoord.out.bam		ENCORE2	18498
RPS15A-BGHcLV32-65_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65/Aligned.sortedByCoord.out.bam		ENCORE2	18552
RPS15A-BGHcLV32-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65/Aligned.sortedByCoord.out.bam		ENCORE2	18606
RPS15A-BGHcLV32-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65/Aligned.sortedByCoord.out.bam		ENCORE2	18660
RPS15A-BGHcLV32-65_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2023					GRCh38	V40	RPS15A-BGHcLV32-65_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGHcLV32-65_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18714
RPS15A-BGHcLV32-66_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2024	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6524
RPS15A-BGHcLV32-66_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2024	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6578
RPS15A-BGHcLV32-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGHcLV32-66_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18445
RPS15A-BGHcLV32-66_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66/Aligned.sortedByCoord.out.bam		ENCORE2	18499
RPS15A-BGHcLV32-66_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66/Aligned.sortedByCoord.out.bam		ENCORE2	18553
RPS15A-BGHcLV32-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66/Aligned.sortedByCoord.out.bam		ENCORE2	18607
RPS15A-BGHcLV32-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66/Aligned.sortedByCoord.out.bam		ENCORE2	18661
RPS15A-BGHcLV32-66_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2024					GRCh38	V40	RPS15A-BGHcLV32-66_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15A-BGHcLV32-66_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18715