PRPF6 RNA-Seq in HepG2

General Information


RBP	PRPF6
Cell_Line	HepG2
Method	shRNA
Exp_Name	PRPF6-BGHLV14-HepG2
ENCODE_series_ID	ENCSR196YEP
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR529QEZ
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	PRPF6_BGHLV14-31
Rep2	PRPF6_BGHLV14-32
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	55.7
Rep2_qPCR	63.5
Rep1_WB	49.7
Rep2_WB	52.5
Antibody Cat#	A302-773A
Antibody Lot#	A302-773A
Antibody DCC ID	ENCAB729OTZ
Status	Released
Project	ENCODE3
ID	398

Experiment Information (Status: Released)

	BGHLV14-31	BGHLV14-32
idx	127	128
TRCN#_or_BGC#	TRCN0000074634	TRCN0000074634
shRNA_or_gRNA_sequence	GCGTACTTCGAGAAGAACCAT	GCGTACTTCGAGAAGAACCAT
PAM
Name	PRPF6	PRPF6
Sample_ID	BGHLV14-31	BGHLV14-32
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	PRPF6	PRPF6
qPCR_result	55.7	63.5
Ave_qPCR	59.6
RT-qPCR_primer-F	gttggggaccagatgaagaa
RT-qPCR_primer-R	gagaagaggctcccagcata
protein_conc	3434	4148
WB_result	49.7	52.5
Ave_WB	51.1
WB_DONE_date
MW	107kDa
IP	1	1
antibody_Cat#	A302-773A	A302-773A
Antibody DCC ID	ENCAB729OTZ	ENCAB729OTZ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	85.2	0
Rep2_TPM	81.5	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2188	2189

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PRPF6	Product_ID: A302-773A Lot_ID: 1 Source: Bethyl Labs Target Name: PRPF6-human

Experiment Status

	BGHLV14-31	BGHLV14-32
Sample_ID	BGHLV14-31	BGHLV14-32
Sample Name	PRPF6_BGHLV14-31	PRPF6_BGHLV14-32
Sample Name	PRPF6_BGHLV14-31	PRPF6_BGHLV14-32
RBP	PRPF6	PRPF6
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	522	523

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-31	BGHLV14-32
Sample #
Sample Name	PRPF6-BGHLV14-31	PRPF6-BGHLV14-32
Sample_Name_Alias	PRPF6_BGHLV14-31	PRPF6_BGHLV14-32
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F11.png	DNA_Library_LV13-14/set1/G11.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G7.png	RNA_Library_LV13-14-16/set1/H7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-31	BGHLV14-32
RBP	PRPF6	PRPF6
Batch_ID	BGHLV14	BGHLV14
WB_result	49.700	52.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2204	2205

Sequencing Information

	BGHLV14-31	BGHLV14-32
Sample_ID	BGHLV14-31	BGHLV14-32
Sample Name	PRPF6_BGHLV14-31	PRPF6_BGHLV14-32
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	55,340,000	52,910,000
total_aligned_reads	49,401,908	47,843,888
unique_aligned_reads	46,493,120	45,066,136
percent_uniqueAligned	0.84014	0.85175
correlation_replicates	0.995915	0.995915
spikein_reads	490,496	307,252
percent_spikeins	0.00886	0.00581
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	846	847

Data Submission Information

	BGHLV14-31	BGHLV14-31
ENCODE_alias	brenton-graveley:PRPF6_BGHLV14	brenton-graveley:PRPF6-BGHLV14-HepG2
ENCODE_accession	ENCSR529QEZ	ENCSR196YEP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-31	BGHLV14-31
Sample Name	PRPF6_BGHLV14-31	PRPF6_BGHLV14-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2810	6868

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
PRPF6_BGHLV14-31_AGTCAA_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	846	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13814
PRPF6_BGHLV14-31_AGTCAA_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	846	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13876
PRPF6_BGHLV14-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31_AGTCAA_L004_R1_001.fastq.gz,PRPF6_BGHLV14-31_AGTCAA_L004_R2_001.fastq.gz		ENCORE2	13938
PRPF6_BGHLV14-31_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31/Aligned.sortedByCoord.out.bam		ENCORE2	14000
PRPF6_BGHLV14-31_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31/Aligned.sortedByCoord.out.bam		ENCORE2	14062
PRPF6_BGHLV14-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31/Aligned.sortedByCoord.out.bam		ENCORE2	14124
PRPF6_BGHLV14-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31/Aligned.sortedByCoord.out.bam		ENCORE2	14186
PRPF6_BGHLV14-31_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	846					GRCh38	V40	PRPF6_BGHLV14-31_AGTCAA_L004_R1_001.fastq.gz,PRPF6_BGHLV14-31_AGTCAA_L004_R2_001.fastq.gz		ENCORE2	14248
PRPF6_BGHLV14-32_AGTTCC_L004_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	847	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13815
PRPF6_BGHLV14-32_AGTTCC_L004_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	847	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13877
PRPF6_BGHLV14-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32_AGTTCC_L004_R1_001.fastq.gz,PRPF6_BGHLV14-32_AGTTCC_L004_R2_001.fastq.gz		ENCORE2	13939
PRPF6_BGHLV14-32_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32/Aligned.sortedByCoord.out.bam		ENCORE2	14001
PRPF6_BGHLV14-32_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32/Aligned.sortedByCoord.out.bam		ENCORE2	14063
PRPF6_BGHLV14-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32/Aligned.sortedByCoord.out.bam		ENCORE2	14125
PRPF6_BGHLV14-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32/Aligned.sortedByCoord.out.bam		ENCORE2	14187
PRPF6_BGHLV14-32_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	847					GRCh38	V40	PRPF6_BGHLV14-32_AGTTCC_L004_R1_001.fastq.gz,PRPF6_BGHLV14-32_AGTTCC_L004_R2_001.fastq.gz		ENCORE2	14249