PRPF3 RNA-Seq in HepG2

General Information


RBP	PRPF3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PRPF3-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR100SUZ
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR909TFJ
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	PRPF3-BGHcLV22-39
Rep2	PRPF3-BGHcLV22-40
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	58.5
Rep2_WB	61.4
Antibody Cat#	A302-073A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB940XJC
Status	Released
Project	ENCODE4
ID	46

Experiment Information (Status: Released)

	BGHcLV22-39	BGHcLV22-40
idx	632	633
TRCN#_or_BGC#	BGC#0000533	BGC#0000533
shRNA_or_gRNA_sequence	ACGAATACCCCGTTTTGAGG	ACGAATACCCCGTTTTGAGG
PAM	AGG	AGG
Name	PRPF3_92	PRPF3_92
Sample_ID	BGHcLV22-39	BGHcLV22-40
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	PRPF3	PRPF3
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGAAATTGAGTGGTGGGACTCT
RT-qPCR_primer-R	GGGCTGGATGTTCAACAAGA
protein_conc	1654	2010
WB_result	58.5	61.4
Ave_WB	59.9
WB_DONE_date	9/2/20-2	JESS
MW	77.5kDa
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	6787	6788

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

	BGHcLV22-39	BGHcLV22-40
Sample_ID	BGHcLV22-39	BGHcLV22-40
Sample Name
Sample Name	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-40
RBP	PRPF3	PRPF3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7385	7386

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-39	BGHcLV22-40
Sample #	21	22
Sample Name	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-40
Sample_Name_Alias
Index Well Position	E03	F03
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	300	293
Peak_Molarity	83.20	165.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E3.png	DNA_Library_set46/set1/F3.png
RIN	9.5	9.8
libSample_RNA_Well	RNA_Library_set46/set1/E11.png	RNA_Library_set46/set3/E12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-39	BGHcLV22-40
RBP	PRPF3	PRPF3
Batch_ID	BGHcLV22	BGHcLV22
WB_result	58.500	61.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1396	1397

Sequencing Information

	BGHcLV22-39	BGHcLV22-40
Sample_ID	BGHcLV22-39	BGHcLV22-40
Sample Name	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-40
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	160,991,176	111,471,390
total_aligned_reads	120,386,614	97,511,212
unique_aligned_reads	112,568,544	91,313,838
percent_uniqueAligned	0.69922	0.81917
correlation_replicates	0.996537	0.996537
spikein_reads	51,608	44,450
percent_spikeins	0.00032	0.00040
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	502	503

Data Submission Information

	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-40	BGHcLV22-40	BGHcLV22-40	BGHcLV22-40
ENCODE_alias	brenton-graveley:PRPF3-BGHcLV22	brenton-graveley:PRPF3-BGHcLV22-39	brenton-graveley:L-PRPF3-BGHcLV22-39	brenton-graveley:PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGHcLV22-HepG2	brenton-graveley:PRPF3-BGHcLV22-40	brenton-graveley:L-PRPF3-BGHcLV22-40	brenton-graveley:PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR909TFJ	ENCBS615UGH	ENCLB249WNR	ENCFF564MFW	ENCFF433MIX	ENCSR100SUZ	ENCBS607OAV	ENCLB929ICY	ENCFF201NZA	ENCFF730BLK
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	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-39	BGHcLV22-40	BGHcLV22-40	BGHcLV22-40	BGHcLV22-40
Sample Name	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-39	PRPF3-BGHcLV22-40	PRPF3-BGHcLV22-40	PRPF3-BGHcLV22-40	PRPF3-BGHcLV22-40
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
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		PRPF3-BGHcLV22-39.pdf	L-PRPF3-BGHcLV22-39.pdf				PRPF3-BGHcLV22-40.pdf	L-PRPF3-BGHcLV22-40.pdf
ID	2405	2447	2511	2575	2605	7287	2448	2512	2576	2606

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-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	502	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1368
PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	502	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1432
PRPF3-BGHcLV22-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25271
PRPF3-BGHcLV22-39_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGHcLV22-39_GGTACCTT+GACGTCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25369
PRPF3-BGHcLV22-39_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	26019
PRPF3-BGHcLV22-39_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	26049
PRPF3-BGHcLV22-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	26079
PRPF3-BGHcLV22-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	502					GRCh38	V40	PRPF3-BGHcLV22-39/Aligned.sortedByCoord.out.bam		ENCORE2	26109
PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	503	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1369
PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	503	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1433
PRPF3-BGHcLV22-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25272
PRPF3-BGHcLV22-40_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF3-BGHcLV22-40_AACGTTCC+AGTACTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25370
PRPF3-BGHcLV22-40_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	26020
PRPF3-BGHcLV22-40_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	26050
PRPF3-BGHcLV22-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	26080
PRPF3-BGHcLV22-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	503					GRCh38	V40	PRPF3-BGHcLV22-40/Aligned.sortedByCoord.out.bam		ENCORE2	26110