RPS9 RNA-Seq in K562

General Information


RBP	RPS9
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS9-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	RPS9-BGKcLV46-77B
Rep2	RPS9-BGKcLV46-78B
CN1	NT-BGKcLV46-1B
CN2	NT-BGKcLV46-2B
Rep1_qPCR	xx
Rep2_qPCR	xx
Rep1_WB	63.5
Rep2_WB	74.8
Antibody Cat#	A303-946A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1657

Experiment Information (Status: Submitting)

	BGKcLV46-77	BGKcLV46-78
idx	0	0
TRCN#_or_BGC#	BGC#0001265	BGC#0001265
shRNA_or_gRNA_sequence	GCGGACCAGCCGCCGCAGCA	GCGGACCAGCCGCCGCAGCA
PAM	GGG	GGG
Name	RPS9_70L	RPS9_70L
Sample_ID	BGKcLV46-77	BGKcLV46-78
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	RPS9	RPS9
qPCR_result	xx	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5142	4342
WB_result	63.5	74.8
Ave_WB
WB_DONE_date	1/15/25
MW	23kd
IP
antibody_Cat#	A303-946A	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	6073	6074

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV46-77	BGKcLV46-77	BGKcLV46-78	BGKcLV46-78
Sample_ID	BGKcLV46-77	BGKcLV46-77	BGKcLV46-78	BGKcLV46-78
Sample Name
Sample Name	RPS9-BGKcLV46-77B	RPS9-BGKcLV46-77B	RPS9-BGKcLV46-78B	RPS9-BGKcLV46-78B
RBP	RPS9	RPS9	RPS9	RPS9
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	Submitting	Submitting	Submitting
Status_date	2025-04-21	2025-04-21	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14058	14146	14059	14147

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-77	BGKcLV46-77	BGKcLV46-78	BGKcLV46-78
Sample #	37	51	38	52
Sample Name	RPS9-BGKcLV46-77	RPS9-BGKcLV46-77B	RPS9-BGKcLV46-78	RPS9-BGKcLV46-78B
Sample_Name_Alias
Index Well Position	E05	C07	F05	D07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	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	156	295	304	287
Peak_Molarity	1.32	85.20	81.20	78.20
libSampleQC_DNA_Well		DNA_Library_set77/set2/C9.png		DNA_Library_set77/set2/D9.png
RIN		9.7		9.8
libSample_RNA_Well		RNA_Library_set77/set1/E5.png		RNA_Library_set77/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-03-04	2025-02-28	2025-03-04
Sample_ID	BGKcLV46-77	BGKcLV46-77	BGKcLV46-78	BGKcLV46-78
RBP	RPS9	RPS9	RPS9	RPS9
Batch_ID	BGKcLV46	BGKcLV46	BGKcLV46	BGKcLV46
WB_result	63.500	63.500	74.800	74.800
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	NotToSequence	SendToSequence	NotToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4696	4710	4697	4711

Sequencing Information

	BGKcLV46-77	BGKcLV46-78
Sample_ID	BGKcLV46-77	BGKcLV46-78
Sample Name	RPS9-BGKcLV46-77B	RPS9-BGKcLV46-78B
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	65,407,111	56,785,253
total_aligned_reads	58,699,783	51,313,646
unique_aligned_reads	54,216,540	47,521,451
percent_uniqueAligned	0.82891	0.83686
correlation_replicates	0.993932	0.993932
spikein_reads	57,810	52,644
percent_spikeins	0.00088	0.00093
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3413	3414

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
RPS9-BGKcLV46-77B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3413	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1B_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2B_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32186
RPS9-BGKcLV46-77B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3413	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1B_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2B_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32236
RPS9-BGKcLV46-77B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3413					GRCh38	V40	RPS9-BGKcLV46-77B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS9-BGKcLV46-77B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32286
RPS9-BGKcLV46-77B_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	3413					GRCh38	V40	RPS9-BGKcLV46-77B_Aligned.sortedByCoord.out.bam		ENCORE2	32336
RPS9-BGKcLV46-77B_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	3413					GRCh38	V40	RPS9-BGKcLV46-77B_Aligned.sortedByCoord.out.bam		ENCORE2	32386
RPS9-BGKcLV46-77B_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	3413					GRCh38	V40	RPS9-BGKcLV46-77B_Aligned.sortedByCoord.out.bam		ENCORE2	32436
RPS9-BGKcLV46-77B_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	3413					GRCh38	V40	RPS9-BGKcLV46-77B_Aligned.sortedByCoord.out.bam		ENCORE2	32486
RPS9-BGKcLV46-77B_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3413					GRCh38	V40	RPS9-BGKcLV46-77B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS9-BGKcLV46-77B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32536
RPS9-BGKcLV46-78B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3414	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1B_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2B_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32187
RPS9-BGKcLV46-78B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3414	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1B_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2B_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32237
RPS9-BGKcLV46-78B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3414					GRCh38	V40	RPS9-BGKcLV46-78B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS9-BGKcLV46-78B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32287
RPS9-BGKcLV46-78B_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	3414					GRCh38	V40	RPS9-BGKcLV46-78B_Aligned.sortedByCoord.out.bam		ENCORE2	32337
RPS9-BGKcLV46-78B_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	3414					GRCh38	V40	RPS9-BGKcLV46-78B_Aligned.sortedByCoord.out.bam		ENCORE2	32387
RPS9-BGKcLV46-78B_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	3414					GRCh38	V40	RPS9-BGKcLV46-78B_Aligned.sortedByCoord.out.bam		ENCORE2	32437
RPS9-BGKcLV46-78B_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	3414					GRCh38	V40	RPS9-BGKcLV46-78B_Aligned.sortedByCoord.out.bam		ENCORE2	32487
RPS9-BGKcLV46-78B_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3414					GRCh38	V40	RPS9-BGKcLV46-78B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPS9-BGKcLV46-78B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32537