RPS12 RNA-Seq in K562

General Information


RBP	RPS12
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS12-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	RPS12-BGKcLV46-69
Rep2	RPS12-BGKcLV46-70
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	0.0
Rep2_qPCR	8.4
Rep1_WB	67.4
Rep2_WB	67.2501
Antibody Cat#	A305-037A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1650

Experiment Information (Status: Submitting)

	BGKcLV46-69	BGKcLV46-70
idx	0	0
TRCN#_or_BGC#	BGC#0001262	BGC#0001262
shRNA_or_gRNA_sequence	TCACCCTTCCTCGGCCATGG	TCACCCTTCCTCGGCCATGG
PAM	CGG	CGG
Name	RPS12_78U	RPS12_78U
Sample_ID	BGKcLV46-69	BGKcLV46-70
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RPS12	RPS12
qPCR_result	0.0	8.4
Ave_qPCR	4.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3734	2868
WB_result	67.4	67.2501
Ave_WB
WB_DONE_date	1/23/24,1/12/25
MW	15kd
IP
antibody_Cat#	A305-037A	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	6065	6066

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS12	Product_ID: A305-037A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS12-human

Experiment Status

	BGKcLV46-69	BGKcLV46-70
Sample_ID	BGKcLV46-69	BGKcLV46-70
Sample Name
Sample Name	RPS12-BGKcLV46-69	RPS12-BGKcLV46-70
RBP	RPS12	RPS12
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14054	14055

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-69	BGKcLV46-70
Sample #	33	34
Sample Name	RPS12-BGKcLV46-69	RPS12-BGKcLV46-70
Sample_Name_Alias
Index Well Position	A05	B05
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	318	304
Peak_Molarity	73.70	72.70
libSampleQC_DNA_Well	DNA_Library_set77/set1/A11.png	DNA_Library_set77/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set77/set1/A5.png	RNA_Library_set77/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-69	BGKcLV46-70
RBP	RPS12	RPS12
Batch_ID	BGKcLV46	BGKcLV46
WB_result	67.400	67.250
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4692	4693

Sequencing Information

	BGKcLV46-69	BGKcLV46-70
Sample_ID	BGKcLV46-69	BGKcLV46-70
Sample Name	RPS12-BGKcLV46-69	RPS12-BGKcLV46-70
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	58,056,670	69,744,702
total_aligned_reads	53,252,235	63,680,902
unique_aligned_reads	49,127,275	58,829,876
percent_uniqueAligned	0.84620	0.84350
correlation_replicates	0.996502	0.996502
spikein_reads	109,348	96,558
percent_spikeins	0.00188	0.00138
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3397	3398

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
RPS12-BGKcLV46-69_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3397	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	32182
RPS12-BGKcLV46-69_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3397	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	32232
RPS12-BGKcLV46-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3397					GRCh38	V40	RPS12-BGKcLV46-69_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS12-BGKcLV46-69_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32282
RPS12-BGKcLV46-69_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	3397					GRCh38	V40	RPS12-BGKcLV46-69_Aligned.sortedByCoord.out.bam		ENCORE2	32332
RPS12-BGKcLV46-69_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	3397					GRCh38	V40	RPS12-BGKcLV46-69_Aligned.sortedByCoord.out.bam		ENCORE2	32382
RPS12-BGKcLV46-69_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	3397					GRCh38	V40	RPS12-BGKcLV46-69_Aligned.sortedByCoord.out.bam		ENCORE2	32432
RPS12-BGKcLV46-69_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	3397					GRCh38	V40	RPS12-BGKcLV46-69_Aligned.sortedByCoord.out.bam		ENCORE2	32482
RPS12-BGKcLV46-69_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3397					GRCh38	V40	RPS12-BGKcLV46-69_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS12-BGKcLV46-69_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32532
RPS12-BGKcLV46-70_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3398	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	32183
RPS12-BGKcLV46-70_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3398	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	32233
RPS12-BGKcLV46-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3398					GRCh38	V40	RPS12-BGKcLV46-70_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS12-BGKcLV46-70_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32283
RPS12-BGKcLV46-70_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	3398					GRCh38	V40	RPS12-BGKcLV46-70_Aligned.sortedByCoord.out.bam		ENCORE2	32333
RPS12-BGKcLV46-70_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	3398					GRCh38	V40	RPS12-BGKcLV46-70_Aligned.sortedByCoord.out.bam		ENCORE2	32383
RPS12-BGKcLV46-70_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	3398					GRCh38	V40	RPS12-BGKcLV46-70_Aligned.sortedByCoord.out.bam		ENCORE2	32433
RPS12-BGKcLV46-70_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	3398					GRCh38	V40	RPS12-BGKcLV46-70_Aligned.sortedByCoord.out.bam		ENCORE2	32483
RPS12-BGKcLV46-70_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3398					GRCh38	V40	RPS12-BGKcLV46-70_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS12-BGKcLV46-70_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32533