PSMD4 RNA-Seq in K562

General Information


RBP	PSMD4
Cell_Line	K562
Method	CRISPR
Exp_Name	PSMD4-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PSMD4-BGKcLV42-73
Rep2	PSMD4-BGKcLV42-74
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	59.2
Rep2_qPCR	54.6
Rep1_WB	90.3
Rep2_WB	92.8
Antibody Cat#	12441S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1555

Experiment Information (Status: Submitting)

	BGKcLV42-73	BGKcLV42-73	BGKcLV42-74	BGKcLV42-74
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001177	BGC#0001177	BGC#0001177	BGC#0001177
shRNA_or_gRNA_sequence	CTTCTGCACGGGCATCCGCG	CTTCTGCACGGGCATCCGCG	CTTCTGCACGGGCATCCGCG	CTTCTGCACGGGCATCCGCG
PAM	TGG	TGG	TGG	TGG
Name	PSMD4_88	PSMD4_88	PSMD4_88	PSMD4_88
Sample_ID	BGKcLV42-73	BGKcLV42-73	BGKcLV42-74	BGKcLV42-74
transduction_Date	4/23/24	4/23/24	4/23/24	4/23/24
days	D6	D6	D6	D6
RBP_name	PSMD4	PSMD4	PSMD4	PSMD4
qPCR_result	59.2	59.2	54.6	54.6
Ave_qPCR	56.9	56.9
RT-qPCR_primer-F	atcattgcctttgtgggaag	atcattgcctttgtgggaag
RT-qPCR_primer-R	tcttgaggcgtttagccagt	tcttgaggcgtttagccagt
protein_conc	2308	2308	2314	2314
WB_result	90.3		92.8
Ave_WB	91.5
WB_DONE_date	5/14/24
MW	50kd	50kd
IP
antibody_Cat#	12441S	3336S	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5837	5839	5838	5840

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PSMD4	Product_ID: 12441S Lot_ID: 1 Source: Cell Signaling Technology Target Name: PSMD4-human

Experiment Status

	BGKcLV42-73	BGKcLV42-73	BGKcLV42-74	BGKcLV42-74
Sample_ID	BGKcLV42-73	BGKcLV42-73	BGKcLV42-74	BGKcLV42-74
Sample Name
Sample Name	PSMD4-BGKcLV42-73		PSMD4-BGKcLV42-74
RBP	PSMD4	PSMD4	PSMD4	PSMD4
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-02-13	2024-06-21	2025-02-13	2024-06-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13104	13150	13105	13151

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-73	BGKcLV42-74
Sample #	61	62
Sample Name	PSMD4-BGKcLV42-73	PSMD4-BGKcLV42-74
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	307	302
Peak_Molarity	106.00	99.30
libSampleQC_DNA_Well	DNA_Library_set73/set1/E8.png	DNA_Library_set73/set1/F8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E8.png	RNA_Library_set73/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-73	BGKcLV42-74
RBP	PSMD4	PSMD4
Batch_ID	BGKcLV42	BGKcLV42
WB_result	90.300	92.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4330	4331

Sequencing Information

	BGKcLV42-73	BGKcLV42-74
Sample_ID	BGKcLV42-73	BGKcLV42-74
Sample Name	PSMD4-BGKcLV42-73	PSMD4-BGKcLV42-74
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	36,920,530	47,024,723
total_aligned_reads	34,520,711	44,545,336
unique_aligned_reads	31,928,139	41,252,519
percent_uniqueAligned	0.86478	0.87725
correlation_replicates	0.998338	0.998338
spikein_reads	2,014	680
percent_spikeins	0.00005	0.00001
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3197	3198

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
PSMD4-BGKcLV42-73_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3197	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30400
PSMD4-BGKcLV42-73_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3197	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30490
PSMD4-BGKcLV42-73_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_L001_R1_001.filtered.trimmed.paired.fastq.gz,PSMD4-BGKcLV42-73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31332
PSMD4-BGKcLV42-73_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_Aligned.sortedByCoord.out.bam		ENCORE2	31422
PSMD4-BGKcLV42-73_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_Aligned.sortedByCoord.out.bam		ENCORE2	31512
PSMD4-BGKcLV42-73_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_Aligned.sortedByCoord.out.bam		ENCORE2	31602
PSMD4-BGKcLV42-73_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_Aligned.sortedByCoord.out.bam		ENCORE2	31692
PSMD4-BGKcLV42-73_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3197					GRCh38	V40	PSMD4-BGKcLV42-73_L001_R1_001.filtered.trimmed.paired.fastq.gz,PSMD4-BGKcLV42-73_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31782
PSMD4-BGKcLV42-74_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3198	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30401
PSMD4-BGKcLV42-74_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3198	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30491
PSMD4-BGKcLV42-74_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_L001_R1_001.filtered.trimmed.paired.fastq.gz,PSMD4-BGKcLV42-74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31333
PSMD4-BGKcLV42-74_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_Aligned.sortedByCoord.out.bam		ENCORE2	31423
PSMD4-BGKcLV42-74_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_Aligned.sortedByCoord.out.bam		ENCORE2	31513
PSMD4-BGKcLV42-74_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_Aligned.sortedByCoord.out.bam		ENCORE2	31603
PSMD4-BGKcLV42-74_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_Aligned.sortedByCoord.out.bam		ENCORE2	31693
PSMD4-BGKcLV42-74_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3198					GRCh38	V40	PSMD4-BGKcLV42-74_L001_R1_001.filtered.trimmed.paired.fastq.gz,PSMD4-BGKcLV42-74_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31783