RPS19 RNA-Seq in K562

General Information


RBP	RPS19
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS19-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPS19-BGKcLV46-73
Rep2	RPS19-BGKcLV46-74
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	61.0
Rep2_qPCR	64.4
Rep1_WB	48.8
Rep2_WB	50.6
Antibody Cat#	A304-002A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1651

Experiment Information (Status: Submitting)

	BGKcLV46-73	BGKcLV46-74
idx	0	0
TRCN#_or_BGC#	BGC#0001095	BGC#0001095
shRNA_or_gRNA_sequence	CAACCCCAGCGCCACCCCGG	CAACCCCAGCGCCACCCCGG
PAM	agg	agg
Name	RPS19_51	RPS19_51
Sample_ID	BGKcLV46-73	BGKcLV46-74
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RPS19	RPS19
qPCR_result	61.0	64.4
Ave_qPCR	62.7
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3239	3643
WB_result	48.8	50.6
Ave_WB
WB_DONE_date	1/15/25,1/23/25
MW	16kd
IP
antibody_Cat#	A304-002A	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6069	6070

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS19	Product_ID: A304-002A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS19-human

Experiment Status

	BGKcLV46-73	BGKcLV46-74
Sample_ID	BGKcLV46-73	BGKcLV46-74
Sample Name
Sample Name	RPS19-BGKcLV46-73	RPS19-BGKcLV46-74
RBP	RPS19	RPS19
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14056	14057

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-73	BGKcLV46-74
Sample #	35	36
Sample Name	RPS19-BGKcLV46-73	RPS19-BGKcLV46-74
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	304	300
Peak_Molarity	77.20	31.90
libSampleQC_DNA_Well	DNA_Library_set77/set1/C11.png	DNA_Library_set77/set1/D11.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set77/set1/C5.png	RNA_Library_set77/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-73	BGKcLV46-74
RBP	RPS19	RPS19
Batch_ID	BGKcLV46	BGKcLV46
WB_result	48.800	50.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4694	4695

Sequencing Information

	BGKcLV46-73	BGKcLV46-74
Sample_ID	BGKcLV46-73	BGKcLV46-74
Sample Name	RPS19-BGKcLV46-73	RPS19-BGKcLV46-74
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	63,960,698	41,866,600
total_aligned_reads	59,609,154	37,141,632
unique_aligned_reads	55,176,550	34,371,572
percent_uniqueAligned	0.86266	0.82098
correlation_replicates	0.993108	0.993108
spikein_reads	105,504	32,836
percent_spikeins	0.00165	0.00078
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3399	3400

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
RPS19-BGKcLV46-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3399	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32184
RPS19-BGKcLV46-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3399	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32234
RPS19-BGKcLV46-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS19-BGKcLV46-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32284
RPS19-BGKcLV46-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_Aligned.sortedByCoord.out.bam		ENCORE2	32334
RPS19-BGKcLV46-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_Aligned.sortedByCoord.out.bam		ENCORE2	32384
RPS19-BGKcLV46-73_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_Aligned.sortedByCoord.out.bam		ENCORE2	32434
RPS19-BGKcLV46-73_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_Aligned.sortedByCoord.out.bam		ENCORE2	32484
RPS19-BGKcLV46-73_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3399					GRCh38	V40	RPS19-BGKcLV46-73_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS19-BGKcLV46-73_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32534
RPS19-BGKcLV46-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3400	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32185
RPS19-BGKcLV46-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3400	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32235
RPS19-BGKcLV46-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS19-BGKcLV46-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32285
RPS19-BGKcLV46-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_Aligned.sortedByCoord.out.bam		ENCORE2	32335
RPS19-BGKcLV46-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_Aligned.sortedByCoord.out.bam		ENCORE2	32385
RPS19-BGKcLV46-74_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_Aligned.sortedByCoord.out.bam		ENCORE2	32435
RPS19-BGKcLV46-74_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_Aligned.sortedByCoord.out.bam		ENCORE2	32485
RPS19-BGKcLV46-74_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3400					GRCh38	V40	RPS19-BGKcLV46-74_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS19-BGKcLV46-74_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32535