RPS14 RNA-Seq in K562

General Information


RBP	RPS14
Cell_Line	K562
Method	CRISPR
Exp_Name	RPS14-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RPS14-BGKcLV35-51
Rep2	RPS14-BGKcLV35-52
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	37.9
Rep2_qPCR	38.1
Rep1_WB	50.9
Rep2_WB	52.9
Antibody Cat#	A304-031A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB482NMQ
Status	Submitted
Project	ENCORE2
ID	961

Experiment Information (Status: Submitting)

	BGKcLV35-51	BGKcLV35-52
idx	1328	1329
TRCN#_or_BGC#	BGC#0000811	BGC#0000811
shRNA_or_gRNA_sequence	GCCCGATCTTCATACCCGAG	GCCCGATCTTCATACCCGAG
PAM	CGG	CGG
Name	RPS14_70	RPS14_70
Sample_ID	BGKcLV35-51	BGKcLV35-52
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	RPS14	RPS14
qPCR_result	37.9	38.1
Ave_qPCR	38.0
RT-qPCR_primer-F	gaccaagacccctggacct
RT-qPCR_primer-R	gagtgctgtcagaggggatg
protein_conc	2897	2671
WB_result	50.9	52.9
Ave_WB	51.9
WB_DONE_date	5/12/22
MW	16KD
IP
antibody_Cat#	A304-031A	LOT #1
Antibody DCC ID	ENCAB482NMQ
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5474	5475

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPS14	Product_ID: A304-031A Lot_ID: 1 Source: Bethyl Labs Target Name: RPS14-human

Experiment Status

	BGKcLV35-51	BGKcLV35-52
Sample_ID	BGKcLV35-51	BGKcLV35-52
Sample Name
Sample Name	RPS14-BGKcLV35-51	RPS14-BGKcLV35-52
RBP	RPS14	RPS14
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10879	10880

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-51	BGKcLV35-52
Sample #	45	46
Sample Name	RPS14-BGKcLV35-51	RPS14-BGKcLV35-52
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	284	284
Peak_Molarity	37.80	16.60
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/E10.png	DNA_Library_set54-56/set3/F10.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/E6.png	RNA_Library_set54-56/set2/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-51	BGKcLV35-52
RBP	RPS14	RPS14
Batch_ID	BGKcLV35	BGKcLV35
WB_result	50.900	52.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3362	3363

Sequencing Information

	BGKcLV35-51	BGKcLV35-52
Sample_ID	BGKcLV35-51	BGKcLV35-52
Sample Name	RPS14-BGKcLV35-51	RPS14-BGKcLV35-52
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	60,600,228	66,967,474
total_aligned_reads	56,996,212	63,657,296
unique_aligned_reads	52,476,844	58,818,766
percent_uniqueAligned	0.86595	0.87832
correlation_replicates	0.997480	0.997480
spikein_reads	2,008	3,412
percent_spikeins	0.00003	0.00005
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2241	2242

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
RPS14-BGKcLV35-51_S47_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2241	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8516
RPS14-BGKcLV35-51_S47_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2241	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8566
RPS14-BGKcLV35-51_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51/Aligned.sortedByCoord.out.bam		ENCORE2	17762
RPS14-BGKcLV35-51_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51/Aligned.sortedByCoord.out.bam		ENCORE2	17812
RPS14-BGKcLV35-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51/Aligned.sortedByCoord.out.bam		ENCORE2	17862
RPS14-BGKcLV35-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51/Aligned.sortedByCoord.out.bam		ENCORE2	17912
RPS14-BGKcLV35-51_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51_S47_R1_001.filtered.trimmed.paired.fastq.gz,RPS14-BGKcLV35-51_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17962
RPS14-BGKcLV35-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2241					GRCh38	V40	RPS14-BGKcLV35-51_S47_R1_001.filtered.trimmed.paired.fastq.gz,RPS14-BGKcLV35-51_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29303
RPS14-BGKcLV35-52_S48_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2242	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8517
RPS14-BGKcLV35-52_S48_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2242	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8567
RPS14-BGKcLV35-52_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52/Aligned.sortedByCoord.out.bam		ENCORE2	17763
RPS14-BGKcLV35-52_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52/Aligned.sortedByCoord.out.bam		ENCORE2	17813
RPS14-BGKcLV35-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52/Aligned.sortedByCoord.out.bam		ENCORE2	17863
RPS14-BGKcLV35-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52/Aligned.sortedByCoord.out.bam		ENCORE2	17913
RPS14-BGKcLV35-52_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52_S48_R1_001.filtered.trimmed.paired.fastq.gz,RPS14-BGKcLV35-52_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17963
RPS14-BGKcLV35-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2242					GRCh38	V40	RPS14-BGKcLV35-52_S48_R1_001.filtered.trimmed.paired.fastq.gz,RPS14-BGKcLV35-52_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29304