PSMA1 RNA-Seq in K562

General Information


RBP	PSMA1
Cell_Line	K562
Method	CRISPR
Exp_Name	PSMA1-BGKcLV13-K562
ENCODE_series_ID	ENCSR722XVI
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR058MCC
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	PSMA1-BGKcLV13-61
Rep2	PSMA1-BGKcLV13-62
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	59.5
Rep2_qPCR	60.1
Rep1_WB	62.3
Rep2_WB	67.4
Antibody Cat#	PA1-963
Antibody Lot#	Lot # SD247982
Antibody DCC ID	ENCAB320WSD
Status	Released
Project	ENCODE4
ID	186

Experiment Information (Status: Released)

	BGKcLV13-61	BGKcLV13-62
idx	516	517
TRCN#_or_BGC#	BGC#0000334	BGC#0000334
shRNA_or_gRNA_sequence	CCGCAATTGAGATACCAATA	CCGCAATTGAGATACCAATA
PAM	tgg	tgg
Name	PSMA1_87	PSMA1_87
Sample_ID	BGKcLV13-61	BGKcLV13-62
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	PSMA1	PSMA1
qPCR_result	59.5	60.1
Ave_qPCR	59.8
RT-qPCR_primer-F	GTATCTCAATTGCGGGGCTT
RT-qPCR_primer-R	ATCCAAACACTCCTGACGCA
protein_conc	5527	5284
WB_result	62.3	67.4
Ave_WB	64.9
WB_DONE_date	12/7/18
MW	29KD
IP	Rabbit
antibody_Cat#	PA1-963	Lot # SD247982
Antibody DCC ID	NO ID
submitted_to_DCC_date	3/11/19
Rep1_TPM	219.8	0
Rep2_TPM	226.8	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4624	4625

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PSMA1	Product_ID: PA1-963 Lot_ID: SD247982 Source: Thermo Fisher Target Name: PSMA1-human

Experiment Status

	BGKcLV13-61	BGKcLV13-62
Sample_ID	BGKcLV13-61	BGKcLV13-62
Sample Name	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-62
Sample Name	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-62
RBP	PSMA1	PSMA1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2913	2914

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-61	BGKcLV13-62
Sample #	67	68
Sample Name	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-62
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-C1	2-D1
Tecan	53.68	63.22
Tecan_date	2019-03-18	2019-03-18
Size_bp	274	287
Peak_Molarity	44.10	48.70
libSampleQC_DNA_Well	DNA_Library_set42/set1/C9.png	DNA_Library_set42/set1/D9.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set42/set1/C9.png	RNA_Library_set42/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-61	BGKcLV13-62
RBP	PSMA1	PSMA1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	62.300	67.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	67	68

Sequencing Information

	BGKcLV13-61	BGKcLV13-62
Sample_ID	BGKcLV13-61	BGKcLV13-62
Sample Name	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-62
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	55,325,404	53,358,100
total_aligned_reads	53,546,012	51,392,282
unique_aligned_reads	48,855,304	46,871,986
percent_uniqueAligned	0.88305	0.87844
correlation_replicates	0.998241	0.998241
spikein_reads	41,086	54,224
percent_spikeins	0.00074	0.00102
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	59	60

Data Submission Information

	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-62	BGKcLV13-62	BGKcLV13-62	BGKcLV13-62
ENCODE_alias	brenton-graveley:PSMA1-BGKcLV13	brenton-graveley:PSMA1-BGKcLV13-61	brenton-graveley:L-PSMA1-BGKcLV13-61	brenton-graveley:PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGKcLV13-K562	brenton-graveley:PSMA1-BGKcLV13-62	brenton-graveley:L-PSMA1-BGKcLV13-62	brenton-graveley:PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR058MCC	ENCBS662MSX	ENCLB292IIS	ENCFF647HXX	ENCFF009YFL	ENCSR722XVI	ENCBS903RNW	ENCLB079VKI	ENCFF112WBN	ENCFF687WCJ
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-61	BGKcLV13-62	BGKcLV13-62	BGKcLV13-62	BGKcLV13-62
Sample Name	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-61	PSMA1-BGKcLV13-62	PSMA1-BGKcLV13-62	PSMA1-BGKcLV13-62	PSMA1-BGKcLV13-62
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		PSMA1-BGKcLV13-61.pdf	L-PSMA1-BGKcLV13-61.pdf				PSMA1-BGKcLV13-62.pdf	L-PSMA1-BGKcLV13-62.pdf
ID	785	865	947	1009	1091	7293	866	948	1010	1092

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
PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	59	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	391
PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	59	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	473
PSMA1-BGKcLV13-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23730
PSMA1-BGKcLV13-61_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61/Aligned.sortedByCoord.out.bam		ENCORE2	23812
PSMA1-BGKcLV13-61_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61/Aligned.sortedByCoord.out.bam		ENCORE2	23894
PSMA1-BGKcLV13-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61/Aligned.sortedByCoord.out.bam		ENCORE2	23976
PSMA1-BGKcLV13-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61/Aligned.sortedByCoord.out.bam		ENCORE2	24058
PSMA1-BGKcLV13-61_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	59					GRCh38	V40	PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGKcLV13-61_TTCCTGTT+AGTATCTT_HK3H2DSXX_S67_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24140
PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	60	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	392
PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	60	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	474
PSMA1-BGKcLV13-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23731
PSMA1-BGKcLV13-62_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62/Aligned.sortedByCoord.out.bam		ENCORE2	23813
PSMA1-BGKcLV13-62_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62/Aligned.sortedByCoord.out.bam		ENCORE2	23895
PSMA1-BGKcLV13-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62/Aligned.sortedByCoord.out.bam		ENCORE2	23977
PSMA1-BGKcLV13-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62/Aligned.sortedByCoord.out.bam		ENCORE2	24059
PSMA1-BGKcLV13-62_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	60					GRCh38	V40	PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGKcLV13-62_CCTTCACC+GACGCTCC_HK3H2DSXX_S68_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24141