PES1 RNA-Seq in HepG2

General Information


RBP	PES1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PES1-BGHLV31-HepG2
ENCODE_series_ID	ENCSR291UYQ
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR496ETJ
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	PES1_BGHLV31-45
Rep2	PES1_BGHLV31-46
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	56.9
Rep2_qPCR	52.9
Rep1_WB	58.9
Rep2_WB	56.4
Antibody Cat#	A300-903A
Antibody Lot#	A300-903A
Antibody DCC ID	ENCAB170HXF
Status	Released
Project	ENCODE3
ID	699

Experiment Information (Status: Released)

	BGHLV31-45	BGHLV31-46
idx	793	794
TRCN#_or_BGC#	TRCN0000117725	TRCN0000117725
shRNA_or_gRNA_sequence	GCTTTGTCAACTTCCGCCTTT	GCTTTGTCAACTTCCGCCTTT
PAM
Name	PES1	PES1
Sample_ID	BGHLV31-45	BGHLV31-46
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	PES1	PES1
qPCR_result	56.9	52.9
Ave_qPCR	54.9
RT-qPCR_primer-F	ccaactacatcacccggaac
RT-qPCR_primer-R	aaatgcccttcagaatgcac
protein_conc	4743	4639
WB_result	58.9	56.4
Ave_WB	57.7
WB_DONE_date	12/3/2015
MW	68kDa
IP	1	1
antibody_Cat#	A300-903A	A300-903A
Antibody DCC ID	ENCAB170HXF	ENCAB170HXF
submitted_to_DCC_date	12/7/2015
Rep1_TPM	12.6	0
Rep2_TPM	13.1	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2882	2883

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PES1	Product_ID: A300-903A Lot_ID: 1 Source: Bethyl Labs Target Name: PES1-human

Experiment Status

	BGHLV31-45	BGHLV31-46
Sample_ID	BGHLV31-45	BGHLV31-46
Sample Name	PES1_BGHLV31-45	PES1_BGHLV31-46
Sample Name	PES1_BGHLV31-45	PES1_BGHLV31-46
RBP	PES1	PES1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1127	1128

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-45	BGHLV31-46
Sample #
Sample Name	PES1-BGHLV31-45	PES1-BGHLV31-46
Sample_Name_Alias	PES1_BGHLV31-45	PES1_BGHLV31-46
Index Well Position	S03	S04
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/C7.png	DNA_Library_LV31-21B/set1/D7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C10.png	RNA_Library_LV29-30-31-32/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-45	BGHLV31-46
RBP	PES1	PES1
Batch_ID	BGHLV31	BGHLV31
WB_result	58.900	56.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2824	2825

Sequencing Information

	BGHLV31-45	BGHLV31-46
Sample_ID	BGHLV31-45	BGHLV31-46
Sample Name	PES1_BGHLV31-45	PES1_BGHLV31-46
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	59,420,110	64,369,788
total_aligned_reads	52,696,058	57,268,652
unique_aligned_reads	49,649,876	54,092,512
percent_uniqueAligned	0.83557	0.84034
correlation_replicates	0.993203	0.993203
spikein_reads	259,596	271,102
percent_spikeins	0.00437	0.00421
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1473	1474

Data Submission Information

	BGHLV31-45	BGHLV31-45
ENCODE_alias	brenton-graveley:PES1_BGHLV31	brenton-graveley:PES1-BGHLV31-HepG2
ENCODE_accession	ENCSR496ETJ	ENCSR291UYQ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-45	BGHLV31-45
Sample Name	PES1_BGHLV31-45	PES1_BGHLV31-45
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3096	6853

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_BGHLV31-45_TTAGGC_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1473	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20990
PES1_BGHLV31-45_TTAGGC_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1473	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21016
PES1_BGHLV31-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1473					GRCh38	V40	PES1_BGHLV31-45_TTAGGC_L007_001.R1.fastq.gz,PES1_BGHLV31-45_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	21050
PES1_BGHLV31-45_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	1473					GRCh38	V40	PES1_BGHLV31-45/Aligned.sortedByCoord.out.bam		ENCORE2	21076
PES1_BGHLV31-45_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	1473					GRCh38	V40	PES1_BGHLV31-45/Aligned.sortedByCoord.out.bam		ENCORE2	21102
PES1_BGHLV31-45_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	1473					GRCh38	V40	PES1_BGHLV31-45/Aligned.sortedByCoord.out.bam		ENCORE2	21128
PES1_BGHLV31-45_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	1473					GRCh38	V40	PES1_BGHLV31-45/Aligned.sortedByCoord.out.bam		ENCORE2	21154
PES1_BGHLV31-45_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1473					GRCh38	V40	PES1_BGHLV31-45_TTAGGC_L007_001.R1.fastq.gz,PES1_BGHLV31-45_TTAGGC_L007_001.R2.fastq.gz		ENCORE2	21180
PES1_BGHLV31-46_TGACCA_L007_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1474	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20991
PES1_BGHLV31-46_TGACCA_L007_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1474	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21017
PES1_BGHLV31-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1474					GRCh38	V40	PES1_BGHLV31-46_TGACCA_L007_001.R1.fastq.gz,PES1_BGHLV31-46_TGACCA_L007_001.R2.fastq.gz		ENCORE2	21051
PES1_BGHLV31-46_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	1474					GRCh38	V40	PES1_BGHLV31-46/Aligned.sortedByCoord.out.bam		ENCORE2	21077
PES1_BGHLV31-46_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	1474					GRCh38	V40	PES1_BGHLV31-46/Aligned.sortedByCoord.out.bam		ENCORE2	21103
PES1_BGHLV31-46_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	1474					GRCh38	V40	PES1_BGHLV31-46/Aligned.sortedByCoord.out.bam		ENCORE2	21129
PES1_BGHLV31-46_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	1474					GRCh38	V40	PES1_BGHLV31-46/Aligned.sortedByCoord.out.bam		ENCORE2	21155
PES1_BGHLV31-46_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1474					GRCh38	V40	PES1_BGHLV31-46_TGACCA_L007_001.R1.fastq.gz,PES1_BGHLV31-46_TGACCA_L007_001.R2.fastq.gz		ENCORE2	21181