ESF1 RNA-Seq in HepG2

General Information


RBP	ESF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ESF1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR784YIW
Batch_ID	BGHLV30
Pool ID	Pool-151215A
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR060IWW
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	ESF1_BGHLV30-35
Rep2	ESF1_BGHLV30-36
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	72.1
Rep2_qPCR	56.6
Rep1_WB	64.0
Rep2_WB	61.3
Antibody Cat#	A303-165A
Antibody Lot#	A303-165A
Antibody DCC ID	ENCAB564BXX
Status	Released
Project	ENCODE3
ID	678

Experiment Information (Status: Released)

	BGHLV30-35	BGHLV30-36
idx	721	722
TRCN#_or_BGC#	TRCN0000147185	TRCN0000147185
shRNA_or_gRNA_sequence	CCCTCTGATGTTGATTTGAAT	CCCTCTGATGTTGATTTGAAT
PAM
Name	ESF1/ABTAP	ESF1/ABTAP
Sample_ID	BGHLV30-35	BGHLV30-36
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	ESF1	ESF1
qPCR_result	72.1	56.6
Ave_qPCR	64.4
RT-qPCR_primer-F	ggaacttccctctgatgttga
RT-qPCR_primer-R	tggagatgtgccatcttttg
protein_conc	4703	4133
WB_result	64.0	61.3
Ave_WB	62.6
WB_DONE_date	9/16/2015
MW	117kDa
IP	1	1
antibody_Cat#	A303-165A	A303-165A
Antibody DCC ID	ENCAB564BXX	ENCAB564BXX
submitted_to_DCC_date	12/7/2015
Rep1_TPM	92.6	0
Rep2_TPM	77.6	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2808	2809

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ESF1	Product_ID: A303-165A Lot_ID: 1 Source: Bethyl Labs Target Name: ESF1-human

Experiment Status

	BGHLV30-35	BGHLV30-36
Sample_ID	BGHLV30-35	BGHLV30-36
Sample Name	ESF1_BGHLV30-35	ESF1_BGHLV30-36
Sample Name	ESF1_BGHLV30-35	ESF1_BGHLV30-36
RBP	ESF1	ESF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1054	1055

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-35	BGHLV30-36
Sample #
Sample Name	ESF1-BGHLV30-35	ESF1-BGHLV30-36
Sample_Name_Alias	ESF1_BGHLV30-35	ESF1_BGHLV30-36
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G10.png	DNA_Library_LV35/set1/C5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A6.png	RNA_Library_LV29-30-31-32/set1/B6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-35	BGHLV30-36
RBP	ESF1	ESF1
Batch_ID	BGHLV30	BGHLV30
WB_result	64.000	61.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2746	2747

Sequencing Information

	BGHLV30-35	BGHLV30-36
Sample_ID	BGHLV30-35	BGHLV30-36
Sample Name	ESF1_BGHLV30-35	ESF1_BGHLV30-36
Pool ID	Pool-151215A	Pool-151215A
LocalServer_folder	set30	set30
total_reads	89,359,186	99,232,930
total_aligned_reads	72,046,630	80,754,876
unique_aligned_reads	67,797,110	75,875,320
percent_uniqueAligned	0.75870	0.76462
correlation_replicates	0.998252	0.998252
spikein_reads	243,642	265,752
percent_spikeins	0.00273	0.00268
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1366	1367

Data Submission Information

	BGHLV30-35	BGHLV30-35
ENCODE_alias	brenton-graveley:ESF1_BGHLV30	brenton-graveley:ESF1-BGHLV30-HepG2
ENCODE_accession	ENCSR060IWW	ENCSR784YIW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-35	BGHLV30-35
Sample Name	ESF1_BGHLV30-35	ESF1_BGHLV30-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3076	6697

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
ESF1_BGHLV30-35_CAGATC_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1366	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20712
ESF1_BGHLV30-35_CAGATC_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1366	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20746
ESF1_BGHLV30-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35_CAGATC_L002_001.R1.fastq.gz,ESF1_BGHLV30-35_CAGATC_L002_001.R2.fastq.gz		ENCORE2	20780
ESF1_BGHLV30-35_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	20814
ESF1_BGHLV30-35_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	20848
ESF1_BGHLV30-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	20882
ESF1_BGHLV30-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35/Aligned.sortedByCoord.out.bam		ENCORE2	20916
ESF1_BGHLV30-35_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1366					GRCh38	V40	ESF1_BGHLV30-35_CAGATC_L002_001.R1.fastq.gz,ESF1_BGHLV30-35_CAGATC_L002_001.R2.fastq.gz		ENCORE2	20950
ESF1_BGHLV30-36_ACTTGA_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1367	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20713
ESF1_BGHLV30-36_ACTTGA_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1367	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20747
ESF1_BGHLV30-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36_ACTTGA_L002_001.R1.fastq.gz,ESF1_BGHLV30-36_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	20781
ESF1_BGHLV30-36_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	20815
ESF1_BGHLV30-36_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	20849
ESF1_BGHLV30-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	20883
ESF1_BGHLV30-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36/Aligned.sortedByCoord.out.bam		ENCORE2	20917
ESF1_BGHLV30-36_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1367					GRCh38	V40	ESF1_BGHLV30-36_ACTTGA_L002_001.R1.fastq.gz,ESF1_BGHLV30-36_ACTTGA_L002_001.R2.fastq.gz		ENCORE2	20951