PRPF8 RNA-Seq in HepG2

General Information


RBP	PRPF8
Cell_Line	HepG2
Method	shRNA
Exp_Name	PRPF8-BGHLV17-HepG2
ENCODE_series_ID	ENCSR395JNK
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR998MZP
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	PRPF8_BGHLV17_23
Rep2	PRPF8_BGHLV17_24
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	67.7
Rep2_qPCR	63.3
Rep1_WB	84.1
Rep2_WB	90.1
Antibody Cat#	A303-921A
Antibody Lot#	A303-921A
Antibody DCC ID	ENCAB207WIC
Status	Released
Project	ENCODE3
ID	436

Experiment Information (Status: Released)

	BGHLV17-23	BGHLV17-24
idx	259	260
TRCN#_or_BGC#	TRCN0000075112	TRCN0000075112
shRNA_or_gRNA_sequence	CGCCTCATGAAACATGATGTT	CGCCTCATGAAACATGATGTT
PAM
Name	PRPF8	PRPF8
Sample_ID	BGHLV17-23	BGHLV17-24
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	PRPF8	PRPF8
qPCR_result	67.7	63.3
Ave_qPCR	65.5
RT-qPCR_primer-F	ttttctgggagaaggccagt
RT-qPCR_primer-R	ttgggaatctggttcagtcc
protein_conc	1818	1680
WB_result	84.1	90.1
Ave_WB	87.1
WB_DONE_date	6/4/2015
MW	270kDa
IP	1	1
antibody_Cat#	A303-921A	A303-921A
Antibody DCC ID	ENCAB207WIC	ENCAB207WIC
submitted_to_DCC_date	8/6/2015
Rep1_TPM	71.4	0
Rep2_TPM	69.4	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2324	2325

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF8	Product_ID: A303-921A Lot_ID: 1 Source: Bethyl Labs Target Name: PRPF8-human

Experiment Status

	BGHLV17-23	BGHLV17-24
Sample_ID	BGHLV17-23	BGHLV17-24
Sample Name	PRPF8_BGHLV17_23	PRPF8_BGHLV17_24
Sample Name	PRPF8_BGHLV17_23	PRPF8_BGHLV17_24
RBP	PRPF8	PRPF8
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	600	601

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-23	BGHLV17-24
Sample #
Sample Name	PRPF8-BGHLV17-23	PRPF8-BGHLV17-24
Sample_Name_Alias	PRPF8_BGHLV17_23	PRPF8_BGHLV17_24
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set2/D1.png	DNA_Library_LV16-17/set1/F2.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E4.png	RNA_Library_LV16-17-18/set1/F4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-23	BGHLV17-24
RBP	PRPF8	PRPF8
Batch_ID	BGHLV17	BGHLV17
WB_result	84.100	90.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2284	2285

Sequencing Information

	BGHLV17-23	BGHLV17-24
Sample_ID	BGHLV17-23	BGHLV17-24
Sample Name	PRPF8_BGHLV17_23	PRPF8_BGHLV17_24
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	37,620,000	38,710,000
total_aligned_reads	33,765,896	34,682,446
unique_aligned_reads	31,857,094	32,695,398
percent_uniqueAligned	0.84681	0.84462
correlation_replicates	0.997735	0.997735
spikein_reads	85,636	61,708
percent_spikeins	0.00228	0.00159
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	926	927

Data Submission Information

	BGHLV17-23	BGHLV17-23
ENCODE_alias	brenton-graveley:PRPF8_BGHLV17	brenton-graveley:PRPF8-BGHLV17-HepG2
ENCODE_accession	ENCSR998MZP	ENCSR395JNK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-23	BGHLV17-23
Sample Name	PRPF8_BGHLV17_23	PRPF8_BGHLV17_23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2867	6870

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
PRPF8_BGHLV17_23_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	926	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14508
PRPF8_BGHLV17_23_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	926	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14546
PRPF8_BGHLV17_23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23_AGTCAA_L002_R1_001.fastq.gz,PRPF8_BGHLV17_23_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	14584
PRPF8_BGHLV17_23_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23/Aligned.sortedByCoord.out.bam		ENCORE2	14622
PRPF8_BGHLV17_23_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23/Aligned.sortedByCoord.out.bam		ENCORE2	14660
PRPF8_BGHLV17_23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23/Aligned.sortedByCoord.out.bam		ENCORE2	14698
PRPF8_BGHLV17_23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23/Aligned.sortedByCoord.out.bam		ENCORE2	14736
PRPF8_BGHLV17_23_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	926					GRCh38	V40	PRPF8_BGHLV17_23_AGTCAA_L002_R1_001.fastq.gz,PRPF8_BGHLV17_23_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	14774
PRPF8_BGHLV17_24_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	927	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14509
PRPF8_BGHLV17_24_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	927	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14547
PRPF8_BGHLV17_24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24_AGTTCC_L002_R1_001.fastq.gz,PRPF8_BGHLV17_24_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	14585
PRPF8_BGHLV17_24_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24/Aligned.sortedByCoord.out.bam		ENCORE2	14623
PRPF8_BGHLV17_24_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24/Aligned.sortedByCoord.out.bam		ENCORE2	14661
PRPF8_BGHLV17_24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24/Aligned.sortedByCoord.out.bam		ENCORE2	14699
PRPF8_BGHLV17_24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24/Aligned.sortedByCoord.out.bam		ENCORE2	14737
PRPF8_BGHLV17_24_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	927					GRCh38	V40	PRPF8_BGHLV17_24_AGTTCC_L002_R1_001.fastq.gz,PRPF8_BGHLV17_24_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	14775