ESF1 RNA-Seq in K562

General Information


RBP	ESF1
Cell_Line	K562
Method	shRNA
Exp_Name	ESF1-BGKLV29-K562
ENCODE_series_ID	ENCSR484XYM
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR077BPR
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	ESF1_BGKLV29-31
Rep2	ESF1_BGKLV29-32
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	43.1
Rep2_qPCR	27.0
Rep1_WB	72.2
Rep2_WB	72.6
Antibody Cat#	A303-165A
Antibody Lot#	A303-165A
Antibody DCC ID	ENCAB485WQI
Status	Released
Project	ENCODE3
ID	665

Experiment Information (Status: Released)

	BGKLV29-31	BGKLV29-32
idx	564	565
TRCN#_or_BGC#	TRCN0000147185	TRCN0000147185
shRNA_or_gRNA_sequence	CCCTCTGATGTTGATTTGAAT	CCCTCTGATGTTGATTTGAAT
PAM
Name	ESF1/ABTAP	ESF1/ABTAP
Sample_ID	BGKLV29-31	BGKLV29-32
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	ESF1	ESF1
qPCR_result	43.1	27.0
Ave_qPCR	35.0
RT-qPCR_primer-F	ggaacttccctctgatgttga
RT-qPCR_primer-R	tggagatgtgccatcttttg
protein_conc	3339	2819
WB_result	72.2	72.6
Ave_WB	72.4
WB_DONE_date	9/16/2015
MW	ABTAP	ABTAP
IP	1	1
antibody_Cat#	A303-165A	A303-165A
Antibody DCC ID	ENCAB485WQI	ENCAB485WQI
submitted_to_DCC_date	3/8/2016
Rep1_TPM	20.4718344	0
Rep2_TPM	9.50683115	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	643	644

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

	BGKLV29-31	BGKLV29-32
Sample_ID	BGKLV29-31	BGKLV29-32
Sample Name	ESF1_BGKLV29-31	ESF1_BGKLV29-32
Sample Name	ESF1_BGKLV29-31	ESF1_BGKLV29-32
RBP	ESF1	ESF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1018	1019

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-31	BGKLV29-32
Sample #
Sample Name	ESF1-BGKLV29-31	ESF1-BGKLV29-32
Sample_Name_Alias	ESF1_BGKLV29-31	ESF1_BGKLV29-32
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/A6.png	DNA_Library_LV28-29-30/set1/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/E1.png	RNA_Library_LV29-30-31-32/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-31	BGKLV29-32
RBP	ESF1	ESF1
Batch_ID	BGKLV29	BGKLV29
WB_result	72.200	72.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2708	2709

Sequencing Information

	BGKLV29-31	BGKLV29-32
Sample_ID	BGKLV29-31	BGKLV29-32
Sample Name	ESF1_BGKLV29-31	ESF1_BGKLV29-32
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	66,428,258	91,069,570
total_aligned_reads	47,360,028	69,442,852
unique_aligned_reads	43,313,696	63,441,928
percent_uniqueAligned	0.65204	0.69663
correlation_replicates	0.995256	0.995256
spikein_reads	224,832	289,526
percent_spikeins	0.00338	0.00318
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1350	1351

Data Submission Information

	BGKLV29-31	BGKLV29-31
ENCODE_alias	brenton-graveley:ESF1_BGKLV29	brenton-graveley:ESF1-BGKLV29-K562
ENCODE_accession	ENCSR077BPR	ENCSR484XYM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-31	BGKLV29-31
Sample Name	ESF1_BGKLV29-31	ESF1_BGKLV29-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3058	6698

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_BGKLV29-31_GTCCGC_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1350	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20420
ESF1_BGKLV29-31_GTCCGC_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1350	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20450
ESF1_BGKLV29-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31_GTCCGC_L005_001.R1.fastq.gz,ESF1_BGKLV29-31_GTCCGC_L005_001.R2.fastq.gz		ENCORE2	20480
ESF1_BGKLV29-31_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31/Aligned.sortedByCoord.out.bam		ENCORE2	20510
ESF1_BGKLV29-31_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31/Aligned.sortedByCoord.out.bam		ENCORE2	20540
ESF1_BGKLV29-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31/Aligned.sortedByCoord.out.bam		ENCORE2	20570
ESF1_BGKLV29-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31/Aligned.sortedByCoord.out.bam		ENCORE2	20600
ESF1_BGKLV29-31_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1350					GRCh38	V40	ESF1_BGKLV29-31_GTCCGC_L005_001.R1.fastq.gz,ESF1_BGKLV29-31_GTCCGC_L005_001.R2.fastq.gz		ENCORE2	20630
ESF1_BGKLV29-32_GTGAAA_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1351	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20421
ESF1_BGKLV29-32_GTGAAA_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1351	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20451
ESF1_BGKLV29-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32_GTGAAA_L005_001.R1.fastq.gz,ESF1_BGKLV29-32_GTGAAA_L005_001.R2.fastq.gz		ENCORE2	20481
ESF1_BGKLV29-32_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32/Aligned.sortedByCoord.out.bam		ENCORE2	20511
ESF1_BGKLV29-32_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32/Aligned.sortedByCoord.out.bam		ENCORE2	20541
ESF1_BGKLV29-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32/Aligned.sortedByCoord.out.bam		ENCORE2	20571
ESF1_BGKLV29-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32/Aligned.sortedByCoord.out.bam		ENCORE2	20601
ESF1_BGKLV29-32_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1351					GRCh38	V40	ESF1_BGKLV29-32_GTGAAA_L005_001.R1.fastq.gz,ESF1_BGKLV29-32_GTGAAA_L005_001.R2.fastq.gz		ENCORE2	20631