PUS1 RNA-Seq in HepG2

General Information


RBP	PUS1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PUS1-BGHLV31-HepG2
ENCODE_series_ID	ENCSR726PDN
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR296ERI
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	PUS1_BGHLV31-51
Rep2	PUS1_BGHLV31-52
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	57.0
Rep2_qPCR	51.3
Rep1_WB	83.3
Rep2_WB	79.6
Antibody Cat#	A301-651A
Antibody Lot#	A301-651A
Antibody DCC ID	ENCAB680DCY
Status	Released
Project	ENCODE3
ID	700

Experiment Information (Status: Released)

	BGHLV31-51	BGHLV31-52
idx	799	800
TRCN#_or_BGC#	TRCN0000045517	TRCN0000045517
shRNA_or_gRNA_sequence	GCACTTCGAGAAGTACAACCA	GCACTTCGAGAAGTACAACCA
PAM
Name	PUS1	PUS1
Sample_ID	BGHLV31-51	BGHLV31-52
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	PUS1	PUS1
qPCR_result	57.0	51.3
Ave_qPCR	54.2
RT-qPCR_primer-F	gtgctgctcatggcctattc
RT-qPCR_primer-R	cggacaccaagtcatcttca
protein_conc	2962	3674
WB_result	83.3	79.6
Ave_WB	81.5
WB_DONE_date	11/18/2015
MW	47kDa
IP	1	1
antibody_Cat#	A301-651A	A301-651A
Antibody DCC ID	ENCAB680DCY	ENCAB680DCY
submitted_to_DCC_date	12/7/2015
Rep1_TPM	6.4	0
Rep2_TPM	8.3	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2888	2889

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUS1	Product_ID: A301-651A Lot_ID: 1 Source: Bethyl Labs Target Name: PUS1-human

Experiment Status

	BGHLV31-51	BGHLV31-52
Sample_ID	BGHLV31-51	BGHLV31-52
Sample Name	PUS1_BGHLV31-51	PUS1_BGHLV31-52
Sample Name	PUS1_BGHLV31-51	PUS1_BGHLV31-52
RBP	PUS1	PUS1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1129	1130

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-51	BGHLV31-52
Sample #
Sample Name	PUS1-BGHLV31-51	PUS1-BGHLV31-52
Sample_Name_Alias	PUS1_BGHLV31-51	PUS1_BGHLV31-52
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/E7.png	DNA_Library_LV31-21B/set1/F7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E10.png	RNA_Library_LV29-30-31-32/set1/F10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-51	BGHLV31-52
RBP	PUS1	PUS1
Batch_ID	BGHLV31	BGHLV31
WB_result	83.300	79.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2826	2827

Sequencing Information

	BGHLV31-51	BGHLV31-52
Sample_ID	BGHLV31-51	BGHLV31-52
Sample Name	PUS1_BGHLV31-51	PUS1_BGHLV31-52
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	59,266,344	64,610,978
total_aligned_reads	53,876,742	57,764,742
unique_aligned_reads	50,866,426	54,468,818
percent_uniqueAligned	0.85827	0.84303
correlation_replicates	0.999551	0.999551
spikein_reads	263,176	289,652
percent_spikeins	0.00444	0.00448
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1475	1476

Data Submission Information

	BGHLV31-51	BGHLV31-51
ENCODE_alias	brenton-graveley:PUS1_BGHLV31	brenton-graveley:PUS1-BGHLV31-HepG2
ENCODE_accession	ENCSR296ERI	ENCSR726PDN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-51	BGHLV31-51
Sample Name	PUS1_BGHLV31-51	PUS1_BGHLV31-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3097	6883

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
PUS1_BGHLV31-51_ACAGTG_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1475	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20992
PUS1_BGHLV31-51_ACAGTG_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1475	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21018
PUS1_BGHLV31-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51_ACAGTG_L007_001.R1.fastq.gz,PUS1_BGHLV31-51_ACAGTG_L007_001.R2.fastq.gz		ENCORE2	21052
PUS1_BGHLV31-51_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51/Aligned.sortedByCoord.out.bam		ENCORE2	21078
PUS1_BGHLV31-51_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51/Aligned.sortedByCoord.out.bam		ENCORE2	21104
PUS1_BGHLV31-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51/Aligned.sortedByCoord.out.bam		ENCORE2	21130
PUS1_BGHLV31-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51/Aligned.sortedByCoord.out.bam		ENCORE2	21156
PUS1_BGHLV31-51_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1475					GRCh38	V40	PUS1_BGHLV31-51_ACAGTG_L007_001.R1.fastq.gz,PUS1_BGHLV31-51_ACAGTG_L007_001.R2.fastq.gz		ENCORE2	21182
PUS1_BGHLV31-52_GCCAAT_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1476	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20993
PUS1_BGHLV31-52_GCCAAT_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1476	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21019
PUS1_BGHLV31-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52_GCCAAT_L007_001.R1.fastq.gz,PUS1_BGHLV31-52_GCCAAT_L007_001.R2.fastq.gz		ENCORE2	21053
PUS1_BGHLV31-52_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52/Aligned.sortedByCoord.out.bam		ENCORE2	21079
PUS1_BGHLV31-52_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52/Aligned.sortedByCoord.out.bam		ENCORE2	21105
PUS1_BGHLV31-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52/Aligned.sortedByCoord.out.bam		ENCORE2	21131
PUS1_BGHLV31-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52/Aligned.sortedByCoord.out.bam		ENCORE2	21157
PUS1_BGHLV31-52_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1476					GRCh38	V40	PUS1_BGHLV31-52_GCCAAT_L007_001.R1.fastq.gz,PUS1_BGHLV31-52_GCCAAT_L007_001.R2.fastq.gz		ENCORE2	21183