RPS15 RNA-Seq in HepG2

General Information


RBP	RPS15
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPS15-BGHcLV36-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV36
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPS15-BGHcLV36-65
Rep2	RPS15-BGHcLV36-66
CN1	NT-BGHcLV36-1
CN2	NT-BGHcLV36-2
Rep1_qPCR	69.2
Rep2_qPCR	69.4
Rep1_WB	52.7
Rep2_WB	51.3
Antibody Cat#	A305-041A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1049

Experiment Information (Status: Submitting)

	BGHcLV36-65	BGHcLV36-65	BGHcLV36-66	BGHcLV36-66
idx	1196	0	1197	0
TRCN#_or_BGC#	BGC#0000812	BGC#0000812	BGC#0000812	BGC#0000812
shRNA_or_gRNA_sequence	CTCCCGCAGCCCGAGATGAT	CTCCCGCAGCCCGAGATGAT	CTCCCGCAGCCCGAGATGAT	CTCCCGCAGCCCGAGATGAT
PAM	CGG	CGG	CGG	CGG
Name	RPS15-92	RPS15-92	RPS15-92	RPS15-92
Sample_ID	BGHcLV36-65	BGHcLV36-65	BGHcLV36-66	BGHcLV36-66
transduction_Date	8/2/22	8/2/22	8/2/22	8/2/22
days	D6	D6	D6	D6
RBP_name	RPS15	RPS15	RPS15	RPS15
qPCR_result	69.2	69.2	69.4	69.4
Ave_qPCR	69.3	69.3
RT-qPCR_primer-F	gaagtggtgaagacgcacct	gaagtggtgaagacgcacct
RT-qPCR_primer-R	caggtagtggccgatcatct	caggtagtggccgatcatct
protein_conc	3688	3688	3274	3274
WB_result	52.7	55.9	51.3	50.6
Ave_WB	52.0	53.2
WB_DONE_date	8/10/22	10/12/22
MW	17KD	17KD
IP
antibody_Cat#	A305-041A	A305-042A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	7381	7383	7382	7384

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS15	Product_ID: A305-041A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS15-human
RPS15	Product_ID: A305-042A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS15-human

Experiment Status

	BGHcLV36-65	BGHcLV36-65	BGHcLV36-66	BGHcLV36-66
Sample_ID	BGHcLV36-65	BGHcLV36-65	BGHcLV36-66	BGHcLV36-66
Sample Name
Sample Name	RPS15-BGHcLV36-65		RPS15-BGHcLV36-66
RBP	RPS15	RPS15	RPS15	RPS15
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2023-04-14	2023-01-03	2023-04-14	2023-01-03
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	10960	11012	10961	11013

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV36-65	BGHcLV36-66
Sample #	19	20
Sample Name	RPS15-BGHcLV36-65	RPS15-BGHcLV36-66
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	296	303
Peak_Molarity	55.80	53.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/C3.png	DNA_Library_set54-56/set1/D3.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set54-56/set1/C3.png	RNA_Library_set54-56/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGHcLV36-65	BGHcLV36-66
RBP	RPS15	RPS15
Batch_ID	BGHcLV36	BGHcLV36
WB_result	52.700	51.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3390	3391

Sequencing Information

	BGHcLV36-65	BGHcLV36-66
Sample_ID	BGHcLV36-65	BGHcLV36-66
Sample Name	RPS15-BGHcLV36-65	RPS15-BGHcLV36-66
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	60,256,172	41,032,326
total_aligned_reads	56,874,818	37,989,452
unique_aligned_reads	53,928,985	36,027,575
percent_uniqueAligned	0.89500	0.87803
correlation_replicates	0.998122	0.998122
spikein_reads	5,306	2,428
percent_spikeins	0.00009	0.00006
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2263	2264

Data Submission Information DCC submission information was not avaliable

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
RPS15-BGHcLV36-65_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2263	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8400
RPS15-BGHcLV36-65_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2263	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8450
RPS15-BGHcLV36-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGHcLV36-65_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25641
RPS15-BGHcLV36-65_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65/Aligned.sortedByCoord.out.bam		ENCORE2	25691
RPS15-BGHcLV36-65_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65/Aligned.sortedByCoord.out.bam		ENCORE2	25741
RPS15-BGHcLV36-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65/Aligned.sortedByCoord.out.bam		ENCORE2	25791
RPS15-BGHcLV36-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65/Aligned.sortedByCoord.out.bam		ENCORE2	25841
RPS15-BGHcLV36-65_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2263					GRCh38	V40	RPS15-BGHcLV36-65_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGHcLV36-65_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25891
RPS15-BGHcLV36-66_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2264	NovaSeq6000	100	paired-ended	1				NT-BGHcLV36-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8401
RPS15-BGHcLV36-66_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2264	NovaSeq6000	100	paired-ended	2				NT-BGHcLV36-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV36-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8451
RPS15-BGHcLV36-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGHcLV36-66_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25642
RPS15-BGHcLV36-66_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66/Aligned.sortedByCoord.out.bam		ENCORE2	25692
RPS15-BGHcLV36-66_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66/Aligned.sortedByCoord.out.bam		ENCORE2	25742
RPS15-BGHcLV36-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66/Aligned.sortedByCoord.out.bam		ENCORE2	25792
RPS15-BGHcLV36-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66/Aligned.sortedByCoord.out.bam		ENCORE2	25842
RPS15-BGHcLV36-66_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2264					GRCh38	V40	RPS15-BGHcLV36-66_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS15-BGHcLV36-66_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25892