PES1 RNA-Seq in HepG2

General Information


RBP	PES1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PES1-BGHLV17-HepG2
ENCODE_series_ID
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR912EHP
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	PES1_BGHLV17_19
Rep2	PES1_BGHLV17_20
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	59.1
Rep2_qPCR	69.1
Rep1_WB	0.0
Rep2_WB	0.0
Antibody Cat#	A300-903A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB170HXF
Status	Archived
Project	ENCODE3
ID	435

Experiment Information (Status: Released)

	BGHLV17-19	BGHLV17-20
idx	255	256
TRCN#_or_BGC#	TRCN0000117724	TRCN0000117724
shRNA_or_gRNA_sequence	CTTATCAAAGACATCAGGTTT	CTTATCAAAGACATCAGGTTT
PAM
Name	PES1	PES1
Sample_ID	BGHLV17-19	BGHLV17-20
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	PES1	PES1
qPCR_result	59.1	69.1
Ave_qPCR	64.1
RT-qPCR_primer-F	ccaactacatcacccggaac
RT-qPCR_primer-R	aaatgcccttcagaatgcac
protein_conc	3391	3009
WB_result	0.0	0.0
Ave_WB	0.0
WB_DONE_date	2/3/2015
MW	68kda
IP	1	1
antibody_Cat#	A300-903A	A300-903A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	12.6	0
Rep2_TPM	13.1	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2320	2321

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV17-19	BGHLV17-20
Sample_ID	BGHLV17-19	BGHLV17-20
Sample Name	PES1_BGHLV17_19	PES1_BGHLV17_20
Sample Name	PES1_BGHLV17_19	PES1_BGHLV17_20
RBP	PES1	PES1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	598	599

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-19	BGHLV17-20
Sample #
Sample Name	PES1-BGHLV17-19	PES1-BGHLV17-20
Sample_Name_Alias	PES1_BGHLV17_19	PES1_BGHLV17_20
Index Well Position	S11	S12
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/B1.png	DNA_Library_LV16-17/set2/C1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C4.png	RNA_Library_LV16-17-18/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-19	BGHLV17-20
RBP	PES1	PES1
Batch_ID	BGHLV17	BGHLV17
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2282	2283

Sequencing Information

	BGHLV17-19	BGHLV17-20
Sample_ID	BGHLV17-19	BGHLV17-20
Sample Name	PES1_BGHLV17_19	PES1_BGHLV17_20
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	34,900,000	109,720,000
total_aligned_reads	30,966,466	98,333,598
unique_aligned_reads	29,263,424	92,840,274
percent_uniqueAligned	0.83849	0.84616
correlation_replicates	0.999151	0.999151
spikein_reads	74,346	174,662
percent_spikeins	0.00213	0.00159
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	924	925

Data Submission Information

	BGHLV17-19
ENCODE_alias	brenton-graveley:PES1_BGHLV17
ENCODE_accession	ENCSR912EHP
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGHLV17-19
Sample Name	PES1_BGHLV17_19
Selected	Yes
Status	Released
Status_Date	2014-12-08
Project	ENCODE3

protocol_URL
ID	2866

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
PES1_BGHLV17_19_GGCTAC_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	924	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	14506
PES1_BGHLV17_19_GGCTAC_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	924	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	14544
PES1_BGHLV17_19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	924					GRCh38	V40	PES1_BGHLV17_19_GGCTAC_L002_R1_001.fastq.gz,PES1_BGHLV17_19_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	14582
PES1_BGHLV17_19_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	924					GRCh38	V40	PES1_BGHLV17_19/Aligned.sortedByCoord.out.bam		ENCORE2	14620
PES1_BGHLV17_19_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	924					GRCh38	V40	PES1_BGHLV17_19/Aligned.sortedByCoord.out.bam		ENCORE2	14658
PES1_BGHLV17_19_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	924					GRCh38	V40	PES1_BGHLV17_19/Aligned.sortedByCoord.out.bam		ENCORE2	14696
PES1_BGHLV17_19_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	924					GRCh38	V40	PES1_BGHLV17_19/Aligned.sortedByCoord.out.bam		ENCORE2	14734
PES1_BGHLV17_19_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	924					GRCh38	V40	PES1_BGHLV17_19_GGCTAC_L002_R1_001.fastq.gz,PES1_BGHLV17_19_GGCTAC_L002_R2_001.fastq.gz		ENCORE2	14772
PES1_BGHLV17_20_CTTGTA_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	925	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	14507
PES1_BGHLV17_20_CTTGTA_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	925	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	14545
PES1_BGHLV17_20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	925					GRCh38	V40	PES1_BGHLV17_20_CTTGTA_L002_R1_001.fastq.gz,PES1_BGHLV17_20_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	14583
PES1_BGHLV17_20_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	925					GRCh38	V40	PES1_BGHLV17_20/Aligned.sortedByCoord.out.bam		ENCORE2	14621
PES1_BGHLV17_20_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	925					GRCh38	V40	PES1_BGHLV17_20/Aligned.sortedByCoord.out.bam		ENCORE2	14659
PES1_BGHLV17_20_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	925					GRCh38	V40	PES1_BGHLV17_20/Aligned.sortedByCoord.out.bam		ENCORE2	14697
PES1_BGHLV17_20_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	925					GRCh38	V40	PES1_BGHLV17_20/Aligned.sortedByCoord.out.bam		ENCORE2	14735
PES1_BGHLV17_20_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	925					GRCh38	V40	PES1_BGHLV17_20_CTTGTA_L002_R1_001.fastq.gz,PES1_BGHLV17_20_CTTGTA_L002_R2_001.fastq.gz		ENCORE2	14773