RPS24 RNA-Seq in K562

Experiment Information (Status: NotSatisfied)

	BGKLV34-35	BGKLV34-36
idx	698	699
TRCN#_or_BGC#	TRCN0000117550	TRCN0000117550
shRNA_or_gRNA_sequence	CGCAAGAACAGAATGAAGAAA	CGCAAGAACAGAATGAAGAAA
PAM
Name	RPS24	RPS24
Sample_ID	BGKLV34-35	BGKLV34-36
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	RPS24	RPS24
qPCR_result	61.8	72.2
Ave_qPCR	67.0
RT-qPCR_primer-F	gcaagacatggcctgtatga
RT-qPCR_primer-R	gcagtccccctgactttctt
protein_conc	2867	2959
WB_result	38.0	33.3
Ave_WB	35.6
WB_DONE_date	2/19/2016
MW	15kd
IP	1	1
antibody_Cat#	A303-842A	A303-842A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	651.93777	0
Rep2_TPM	717.512184	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note	already tried CRISPR; CELL stoped grow after day6
ID	785	786

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV34-35	BGKLV34-36
Sample_ID	BGKLV34-35	BGKLV34-36
Sample Name	RPS24-BGKLV34-35B	RPS24-BGKLV34-36B
Sample Name
RBP	RPS24	RPS24
Cell_Line	K562	K562
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2020-11-04	2020-11-04
Project	ENCODE4	ENCODE4
Note	bad KD%	bad KD%
ID	6459	6460

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-35	BGKLV34-36
Sample #	43	44
Sample Name	RPS24-BGKLV34-35B	RPS24-BGKLV34-36B
Sample_Name_Alias
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	279	293
Peak_Molarity	10.50	10.30
libSampleQC_DNA_Well	DNA_Library_set40/set1/C11.png	DNA_Library_set40/set1/D11.png
RIN	9.1	9.1
libSample_RNA_Well	RNA_Library_set40/set1/A6.png	RNA_Library_set40/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV34-35	BGKLV34-36
RBP	RPS24	RPS24
Batch_ID	BGKLV34	BGKLV34
WB_result	38.000	33.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	966	967

Sequencing Information

	BGKLV34-35	BGKLV34-36
Sample_ID	BGKLV34-35	BGKLV34-36
Sample Name	RPS24-BGKLV34-35B	RPS24-BGKLV34-36B
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	59,120,208	57,689,216
total_aligned_reads	46,501,560	49,840,412
unique_aligned_reads	42,376,976	45,511,806
percent_uniqueAligned	0.71679	0.78891
correlation_replicates	0.997812	0.997812
spikein_reads	10,482	6,242
percent_spikeins	0.00018	0.00011
original_ReadLength	100	100
QC_Status	OtherReasonsNotToSubmit	OtherReasonsNotToSubmit
ID	369	370

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
RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	369	HiSeq2500	100	paired-ended	1				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE4	754
RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	369	HiSeq2500	100	paired-ended	2				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE4	797
RPS24-BGKLV34-35B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R1.fastq.gz,RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23494
RPS24-BGKLV34-35B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B/Aligned.sortedByCoord.out.bam		ENCORE2	23528
RPS24-BGKLV34-35B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B/Aligned.sortedByCoord.out.bam		ENCORE2	23562
RPS24-BGKLV34-35B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B/Aligned.sortedByCoord.out.bam		ENCORE2	23596
RPS24-BGKLV34-35B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B/Aligned.sortedByCoord.out.bam		ENCORE2	23630
RPS24-BGKLV34-35B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	369					GRCh38	V40	RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R1.fastq.gz,RPS24-BGKLV34-35B_TTAGGC_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23664
RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	370	HiSeq2500	100	paired-ended	1				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R1.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R1.fastq.gz	ENCODE4	755
RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	370	HiSeq2500	100	paired-ended	2				NT-BGKLV34-1B_ACTGAT_ACBYWVANXX_L006_001.R2.fastq.gz,NT-BGKLV34-2B_ATTCCT_ACBYWVANXX_L006_001.R2.fastq.gz	ENCODE4	798
RPS24-BGKLV34-36B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R1.fastq.gz,RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23495
RPS24-BGKLV34-36B_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B/Aligned.sortedByCoord.out.bam		ENCORE2	23529
RPS24-BGKLV34-36B_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B/Aligned.sortedByCoord.out.bam		ENCORE2	23563
RPS24-BGKLV34-36B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B/Aligned.sortedByCoord.out.bam		ENCORE2	23597
RPS24-BGKLV34-36B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B/Aligned.sortedByCoord.out.bam		ENCORE2	23631
RPS24-BGKLV34-36B_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	370					GRCh38	V40	RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R1.fastq.gz,RPS24-BGKLV34-36B_TGACCA_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23665