PSMA1 RNA-Seq in HepG2

General Information


RBP	PSMA1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PSMA1-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR148CJC
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR608CUI
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	PSMA1-BGHcLV25-51
Rep2	PSMA1-BGHcLV25-52
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	84.9
Rep2_WB	80.8
Antibody Cat#	PA1-963
Antibody Lot#	SD247982
Antibody DCC ID	ENCAB320WSD
Status	Released
Project	ENCODE4
ID	20

Experiment Information (Status: Released)

	BGHcLV25-51	BGHcLV25-52
idx	758	759
TRCN#_or_BGC#	BGC#0000619	BGC#0000619
shRNA_or_gRNA_sequence	TGATTGGGAACGGGCTCCAA	TGATTGGGAACGGGCTCCAA
PAM	TGG	TGG
Name	PSMA1_87	PSMA1_87
Sample_ID	BGHcLV25-51	BGHcLV25-52
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	PSMA1	PSMA1
qPCR_result	0.0	0.0
Ave_qPCR	0
RT-qPCR_primer-F	GTATCTCAATTGCGGGGCTT
RT-qPCR_primer-R	ATCCAAACACTCCTGACGCA
protein_conc	4743	4814
WB_result	84.9	80.8
Ave_WB	82.8
WB_DONE_date	3/19/21
MW	29KD
IP	Rabbit
antibody_Cat#	PA1-963	SD247982
Antibody DCC ID	ENCAB320WSD
submitted_to_DCC_date	10/26/21
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	8965	8966

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

	BGHcLV25-51	BGHcLV25-52
Sample_ID	BGHcLV25-51	BGHcLV25-52
Sample Name
Sample Name	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-52
RBP	PSMA1	PSMA1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7845	7846

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-51	BGHcLV25-52
Sample #	43	44
Sample Name	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-52
Sample_Name_Alias
Index Well Position	C12	D12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	296	303
Peak_Molarity	209.00	81.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/C9.png	DNA_Library_set47/set1/D9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set1/C6.png	RNA_Library_set47/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-51	BGHcLV25-52
RBP	PSMA1	PSMA1
Batch_ID	BGHcLV25	BGHcLV25
WB_result	84.900	80.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1506	1507

Sequencing Information

	BGHcLV25-51	BGHcLV25-52
Sample_ID	BGHcLV25-51	BGHcLV25-52
Sample Name	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-52
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	92,445,770	114,610,686
total_aligned_reads	86,483,912	108,076,974
unique_aligned_reads	81,202,340	101,418,486
percent_uniqueAligned	0.87838	0.88490
correlation_replicates	0.998268	0.998268
spikein_reads	33,854	19,508
percent_spikeins	0.00037	0.00017
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	588	589

Data Submission Information

	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-52	BGHcLV25-52	BGHcLV25-52	BGHcLV25-52
ENCODE_alias	brenton-graveley:PSMA1-BGHcLV25	brenton-graveley:PSMA1-BGHcLV25-51	brenton-graveley:L-PSMA1-BGHcLV25-51	brenton-graveley:PSMA1-BGHcLV25-51_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGHcLV25-51_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGHcLV25-HepG2	brenton-graveley:PSMA1-BGHcLV25-52	brenton-graveley:L-PSMA1-BGHcLV25-52	brenton-graveley:PSMA1-BGHcLV25-52_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PSMA1-BGHcLV25-52_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR608CUI	ENCBS325UGX	ENCLB968PFX	ENCFF740RLF	ENCFF677PIG	ENCSR148CJC	ENCBS664UYP	ENCLB080RVZ	ENCFF386ICK	ENCFF929ZPM
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	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-51	BGHcLV25-52	BGHcLV25-52	BGHcLV25-52	BGHcLV25-52
Sample Name	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-51	PSMA1-BGHcLV25-52	PSMA1-BGHcLV25-52	PSMA1-BGHcLV25-52	PSMA1-BGHcLV25-52
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-04	2022-02-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2022-02-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		PSMA1-BGHcLV25-51.pdf	L-PSMA1-BGHcLV25-51.pdf				PSMA1-BGHcLV25-52.pdf	L-PSMA1-BGHcLV25-52.pdf
ID	3256	3299	3343	3387	3431	7292	3300	3344	3388	3432

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-BGHcLV25-51_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	588	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3730
PSMA1-BGHcLV25-51_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	588	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3776
PSMA1-BGHcLV25-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGHcLV25-51_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25419
PSMA1-BGHcLV25-51_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGHcLV25-51_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25463
PSMA1-BGHcLV25-51_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51/Aligned.sortedByCoord.out.bam		ENCORE2	26295
PSMA1-BGHcLV25-51_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51/Aligned.sortedByCoord.out.bam		ENCORE2	26339
PSMA1-BGHcLV25-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51/Aligned.sortedByCoord.out.bam		ENCORE2	26383
PSMA1-BGHcLV25-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	588					GRCh38	V40	PSMA1-BGHcLV25-51/Aligned.sortedByCoord.out.bam		ENCORE2	26427
PSMA1-BGHcLV25-52_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	589	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3731
PSMA1-BGHcLV25-52_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	589	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3777
PSMA1-BGHcLV25-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGHcLV25-52_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25420
PSMA1-BGHcLV25-52_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz,PSMA1-BGHcLV25-52_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25464
PSMA1-BGHcLV25-52_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52/Aligned.sortedByCoord.out.bam		ENCORE2	26296
PSMA1-BGHcLV25-52_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52/Aligned.sortedByCoord.out.bam		ENCORE2	26340
PSMA1-BGHcLV25-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52/Aligned.sortedByCoord.out.bam		ENCORE2	26384
PSMA1-BGHcLV25-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	589					GRCh38	V40	PSMA1-BGHcLV25-52/Aligned.sortedByCoord.out.bam		ENCORE2	26428