PSIP1 RNA-Seq in HepG2

General Information


RBP	PSIP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PSIP1-BGHLV18-HepG2
ENCODE_series_ID	ENCSR513SYG
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR744YVR
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	PSIP1_BGHLV18_43
Rep2	PSIP1_BGHLV18_44
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	82.9
Rep2_qPCR	89.7
Rep1_WB	99.9
Rep2_WB	99.6
Antibody Cat#	A300-848A
Antibody Lot#	A300-848A
Antibody DCC ID	ENCAB004FAZ
Status	Released
Project	ENCODE3
ID	455

Experiment Information (Status: Released)

	BGHLV18-43	BGHLV18-44
idx	343	344
TRCN#_or_BGC#	TRCN0000074819	TRCN0000074819
shRNA_or_gRNA_sequence	GCAGCAACTAAACAATCAAAT	GCAGCAACTAAACAATCAAAT
PAM
Name	PSIP1	PSIP1
Sample_ID	BGHLV18-43	BGHLV18-44
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	PSIP1	PSIP1
qPCR_result	82.9	89.7
Ave_qPCR	86.3
RT-qPCR_primer-F	tcaagtcaacaggcagcaac
RT-qPCR_primer-R	gctggctttttcttcatggt
protein_conc	5184	4615
WB_result	99.9	99.6
Ave_WB	99.8
WB_DONE_date	3/31/2015
MW	60kDa
IP	1	1
antibody_Cat#	A300-848A	A300-848A
Antibody DCC ID	ENCAB004FAZ	ENCAB004FAZ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2408	2409

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PSIP1	Product_ID: A300-848A Lot_ID: 1 Source: Bethyl Labs Target Name: PSIP1-human

Experiment Status

	BGHLV18-43	BGHLV18-44
Sample_ID	BGHLV18-43	BGHLV18-44
Sample Name	PSIP1_BGHLV18_43	PSIP1_BGHLV18_44
Sample Name	PSIP1_BGHLV18_43	PSIP1_BGHLV18_44
RBP	PSIP1	PSIP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	640	641

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-43	BGHLV18-44
Sample #
Sample Name	PSIP1-BGHLV18-43	PSIP1-BGHLV18-44
Sample_Name_Alias	PSIP1_BGHLV18_43	PSIP1_BGHLV18_44
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A4.png	DNA_Library_LV18-19/set1/B4.png
RIN	9.3	8.5
libSample_RNA_Well	RNA_Library_LV18-19/set1/G10.png	RNA_Library_LV18-19/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-43	BGHLV18-44
RBP	PSIP1	PSIP1
Batch_ID	BGHLV18	BGHLV18
WB_result	99.900	99.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2324	2325

Sequencing Information

	BGHLV18-43	BGHLV18-44
Sample_ID	BGHLV18-43	BGHLV18-44
Sample Name	PSIP1_BGHLV18_43	PSIP1_BGHLV18_44
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	58,260,000	60,280,000
total_aligned_reads	53,887,988	55,180,432
unique_aligned_reads	50,862,012	52,033,612
percent_uniqueAligned	0.87302	0.86320
correlation_replicates	0.992144	0.992144
spikein_reads	202,566	220,284
percent_spikeins	0.00348	0.00365
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	966	967

Data Submission Information

	BGHLV18-43	BGHLV18-43
ENCODE_alias	brenton-graveley:PSIP1_BGHLV18	brenton-graveley:PSIP1-BGHLV18-HepG2
ENCODE_accession	ENCSR744YVR	ENCSR513SYG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-43	BGHLV18-43
Sample Name	PSIP1_BGHLV18_43	PSIP1_BGHLV18_43
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2837	6872

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
PSIP1_BGHLV18_43_ATCACG_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	966	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14814
PSIP1_BGHLV18_43_ATCACG_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	966	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14852
PSIP1_BGHLV18_43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43_ATCACG_L004_R1_001.fastq.gz,PSIP1_BGHLV18_43_ATCACG_L004_R2_001.fastq.gz		ENCORE2	14890
PSIP1_BGHLV18_43_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43/Aligned.sortedByCoord.out.bam		ENCORE2	14928
PSIP1_BGHLV18_43_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43/Aligned.sortedByCoord.out.bam		ENCORE2	14966
PSIP1_BGHLV18_43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43/Aligned.sortedByCoord.out.bam		ENCORE2	15004
PSIP1_BGHLV18_43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43/Aligned.sortedByCoord.out.bam		ENCORE2	15042
PSIP1_BGHLV18_43_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	966					GRCh38	V40	PSIP1_BGHLV18_43_ATCACG_L004_R1_001.fastq.gz,PSIP1_BGHLV18_43_ATCACG_L004_R2_001.fastq.gz		ENCORE2	15080
PSIP1_BGHLV18_44_CGATGT_L004_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	967	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14815
PSIP1_BGHLV18_44_CGATGT_L004_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	967	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14853
PSIP1_BGHLV18_44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44_CGATGT_L004_R1_001.fastq.gz,PSIP1_BGHLV18_44_CGATGT_L004_R2_001.fastq.gz		ENCORE2	14891
PSIP1_BGHLV18_44_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44/Aligned.sortedByCoord.out.bam		ENCORE2	14929
PSIP1_BGHLV18_44_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44/Aligned.sortedByCoord.out.bam		ENCORE2	14967
PSIP1_BGHLV18_44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44/Aligned.sortedByCoord.out.bam		ENCORE2	15005
PSIP1_BGHLV18_44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44/Aligned.sortedByCoord.out.bam		ENCORE2	15043
PSIP1_BGHLV18_44_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	967					GRCh38	V40	PSIP1_BGHLV18_44_CGATGT_L004_R1_001.fastq.gz,PSIP1_BGHLV18_44_CGATGT_L004_R2_001.fastq.gz		ENCORE2	15081