PRPF3 RNA-Seq in K562

General Information


RBP	PRPF3
Cell_Line	K562
Method	CRISPR
Exp_Name	PRPF3-BGKcLV23-K562
ENCODE_series_ID	ENCSR108XUL
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR681ELF
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	PRPF3-BGKcLV23-55
Rep2	PRPF3-BGKcLV23-56
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	1.0
Rep2_qPCR	0.0
Rep1_WB	63.4
Rep2_WB	65.7
Antibody Cat#	A302-073A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB940XJC
Status	Released
Project	ENCODE4
ID	34

Experiment Information (Status: Released)

	BGKcLV23-55	BGKcLV23-56
idx	841	842
TRCN#_or_BGC#	BGC#0000533	BGC#0000533
shRNA_or_gRNA_sequence	ACGAATACCCCGTTTTGAGG	ACGAATACCCCGTTTTGAGG
PAM	AGG	AGG
Name	PRPF3_92	PRPF3_92
Sample_ID	BGKcLV23-55	BGKcLV23-56
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	PRPF3	PRPF3
qPCR_result	1.0	0.0
Ave_qPCR	0.5
RT-qPCR_primer-F	TGAAATTGAGTGGTGGGACTCT
RT-qPCR_primer-R	GGGCTGGATGTTCAACAAGA
protein_conc	2306	1838
WB_result	63.4	65.7
Ave_WB	64.6
WB_DONE_date	10/2/20	JESS
MW	77.5KD
IP	Rabbit / I
antibody_Cat#	A302-073A	LOT# 2
Antibody DCC ID	ENCAB940XJC
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4973	4974

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF3	Product_ID: A302-073A Lot_ID: 2 Source: Bethyl Labs Target Name: PRPF3-human

Experiment Status

	BGKcLV23-55	BGKcLV23-56
Sample_ID	BGKcLV23-55	BGKcLV23-56
Sample Name
Sample Name	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-56
RBP	PRPF3	PRPF3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7457	7458

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-55	BGKcLV23-56
Sample #	59	60
Sample Name	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-56
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	296	295
Peak_Molarity	125.00	162.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C8.png	DNA_Library_set46/set1/D8.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_set46/set2/C12.png	RNA_Library_set46/set2/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-55	BGKcLV23-56
RBP	PRPF3	PRPF3
Batch_ID	BGKcLV23	BGKcLV23
WB_result	63.400	65.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1434	1435

Sequencing Information

	BGKcLV23-55	BGKcLV23-56
Sample_ID	BGKcLV23-55	BGKcLV23-56
Sample Name	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-56
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	166,005,142	199,881,404
total_aligned_reads	155,849,980	185,480,826
unique_aligned_reads	141,624,434	168,628,362
percent_uniqueAligned	0.85313	0.84364
correlation_replicates	0.998311	0.998311
spikein_reads	71,468	48,420
percent_spikeins	0.00043	0.00024
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	540	541

Data Submission Information

	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-56	BGKcLV23-56	BGKcLV23-56	BGKcLV23-56
ENCODE_alias	brenton-graveley:PRPF3-BGKcLV23	brenton-graveley:PRPF3-BGKcLV23-55	brenton-graveley:L-PRPF3-BGKcLV23-55	brenton-graveley:PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGKcLV23-K562	brenton-graveley:PRPF3-BGKcLV23-56	brenton-graveley:L-PRPF3-BGKcLV23-56	brenton-graveley:PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR681ELF	ENCBS248THI	ENCLB223OQN	ENCFF424GGC	ENCFF112WSV	ENCSR108XUL	ENCBS212CME	ENCLB605DQW	ENCFF453DMB	ENCFF025PTP
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	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-55	BGKcLV23-56	BGKcLV23-56	BGKcLV23-56	BGKcLV23-56
Sample Name	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-55	PRPF3-BGKcLV23-56	PRPF3-BGKcLV23-56	PRPF3-BGKcLV23-56	PRPF3-BGKcLV23-56
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		PRPF3-BGKcLV23-55.pdf	L-PRPF3-BGKcLV23-55.pdf				PRPF3-BGKcLV23-56.pdf	L-PRPF3-BGKcLV23-56.pdf
ID	2424	2485	2549	2643	2677	7288	2486	2550	2644	2678

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
PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	540	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1406
PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	540	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1470
PRPF3-BGKcLV23-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25309
PRPF3-BGKcLV23-55_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGKcLV23-55_GATCTATC+AGCCTCAT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25343
PRPF3-BGKcLV23-55_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55/Aligned.sortedByCoord.out.bam		ENCORE2	26147
PRPF3-BGKcLV23-55_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55/Aligned.sortedByCoord.out.bam		ENCORE2	26181
PRPF3-BGKcLV23-55_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55/Aligned.sortedByCoord.out.bam		ENCORE2	26215
PRPF3-BGKcLV23-55_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	540					GRCh38	V40	PRPF3-BGKcLV23-55/Aligned.sortedByCoord.out.bam		ENCORE2	26249
PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	541	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1407
PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	541	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1471
PRPF3-BGKcLV23-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25310
PRPF3-BGKcLV23-56_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGKcLV23-56_AGCTCGCT+GATTCTGC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25344
PRPF3-BGKcLV23-56_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56/Aligned.sortedByCoord.out.bam		ENCORE2	26148
PRPF3-BGKcLV23-56_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56/Aligned.sortedByCoord.out.bam		ENCORE2	26182
PRPF3-BGKcLV23-56_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56/Aligned.sortedByCoord.out.bam		ENCORE2	26216
PRPF3-BGKcLV23-56_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	541					GRCh38	V40	PRPF3-BGKcLV23-56/Aligned.sortedByCoord.out.bam		ENCORE2	26250