ETF1 RNA-Seq in HepG2

General Information


RBP	ETF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ETF1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR996VFO
Batch_ID	BGHLV37
Pool ID	Pool-161129
Local_Set_Name	set37
ENCODE_KD_Exp_ID	ENCSR840QOH
ENCODE_CN_Exp_ID	ENCSR997HCQ
Rep1	ETF1_BGHLV37-19
Rep2	ETF1_BGHLV37-20
CN1	NT_BGHLV37-1
CN2	NT_BGHLV37-2
Rep1_qPCR	61.1
Rep2_qPCR	68.5
Rep1_WB	55.5
Rep2_WB	50.9
Antibody Cat#	RN111PW
Antibody Lot#	RN111PW
Antibody DCC ID	ENCAB767NXE
Status	Released
Project	ENCODE3
ID	751

Experiment Information (Status: Released)

	BGHLV37-19	BGHLV37-20
idx	931	932
TRCN#_or_BGC#	TRCN0000145565	TRCN0000145565
shRNA_or_gRNA_sequence	GCCTACAACTAAGTTCCTAAA	GCCTACAACTAAGTTCCTAAA
PAM
Name	ETF1	ETF1
Sample_ID	BGHLV37-19	BGHLV37-20
transduction_Date	9/1/16	9/1/16
days
RBP_name	ETF1	ETF1
qPCR_result	61.1	68.5
Ave_qPCR	64.8
RT-qPCR_primer-F	tcagtcctgggagccattac
RT-qPCR_primer-R	caaccagaccatttggaggt
protein_conc	2530	2349
WB_result	55.5	50.9
Ave_WB	53.2
WB_DONE_date	9/19/16
MW	49kDa
IP
antibody_Cat#	RN111PW	RN111PW
Antibody DCC ID	ENCAB767NXE	ENCAB767NXE
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library
Note
ID	3024	3025

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ETF1	Product_ID: RN111PW Lot_ID: 1 Source: MBLI Target Name: ETF1-human

Experiment Status

	BGHLV37-19	BGHLV37-20
Sample_ID	BGHLV37-19	BGHLV37-20
Sample Name	ETF1_BGHLV37-19	ETF1_BGHLV37-20
Sample Name	ETF1_BGHLV37-19	ETF1_BGHLV37-20
RBP	ETF1	ETF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1295	1296

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-19	BGHLV37-20
Sample #
Sample Name	ETF1-BGHLV37-19	ETF1-BGHLV37-20
Sample_Name_Alias	ETF1_BGHLV37-19	ETF1_BGHLV37-20
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2016-11-03
Lib_ID	Lib-161103	Lib-161103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/E3.png	DNA_Library_LV37-38/set1/F3.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_LV37_38/set1/E1.png	RNA_Library_LV37_38/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV37-19	BGHLV37-20
RBP	ETF1	ETF1
Batch_ID	BGHLV37	BGHLV37
WB_result	55.500	50.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2980	2981

Sequencing Information

	BGHLV37-19	BGHLV37-20
Sample_ID	BGHLV37-19	BGHLV37-20
Sample Name	ETF1_BGHLV37-19	ETF1_BGHLV37-20
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set37	set37
total_reads	130,000,000	68,191,490
total_aligned_reads	117,247,180	62,530,836
unique_aligned_reads	109,766,268	58,755,172
percent_uniqueAligned	0.84436	0.86162
correlation_replicates	0.998560	0.998560
spikein_reads	292,588	198,308
percent_spikeins	0.00225	0.00291
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1629	1630

Data Submission Information

	BGHLV37-19	BGHLV37-19
ENCODE_alias	brenton-graveley:ETF1_BGHLV37	brenton-graveley:ETF1-BGHLV37-HepG2
ENCODE_accession	ENCSR840QOH	ENCSR996VFO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-19	BGHLV37-19
Sample Name	ETF1_BGHLV37-19	ETF1_BGHLV37-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3187	6699

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
ETF1_BGHLV37-19_CGTACG_L005_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1629	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22036
ETF1_BGHLV37-19_CGTACG_L005_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1629	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22052
ETF1_BGHLV37-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19_CGTACG_L005_001.R1.fastq.gz,ETF1_BGHLV37-19_CGTACG_L005_001.R2.fastq.gz		ENCORE2	22068
ETF1_BGHLV37-19_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19/Aligned.sortedByCoord.out.bam		ENCORE2	22084
ETF1_BGHLV37-19_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19/Aligned.sortedByCoord.out.bam		ENCORE2	22100
ETF1_BGHLV37-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19/Aligned.sortedByCoord.out.bam		ENCORE2	22116
ETF1_BGHLV37-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19/Aligned.sortedByCoord.out.bam		ENCORE2	22132
ETF1_BGHLV37-19_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1629					GRCh38	V40	ETF1_BGHLV37-19_CGTACG_L005_001.R1.fastq.gz,ETF1_BGHLV37-19_CGTACG_L005_001.R2.fastq.gz		ENCORE2	22148
ETF1_BGHLV37-20_GAGTGG_L005_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1630	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22037
ETF1_BGHLV37-20_GAGTGG_L005_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1630	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22053
ETF1_BGHLV37-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20_GAGTGG_L005_001.R1.fastq.gz,ETF1_BGHLV37-20_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	22069
ETF1_BGHLV37-20_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20/Aligned.sortedByCoord.out.bam		ENCORE2	22085
ETF1_BGHLV37-20_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20/Aligned.sortedByCoord.out.bam		ENCORE2	22101
ETF1_BGHLV37-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20/Aligned.sortedByCoord.out.bam		ENCORE2	22117
ETF1_BGHLV37-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20/Aligned.sortedByCoord.out.bam		ENCORE2	22133
ETF1_BGHLV37-20_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1630					GRCh38	V40	ETF1_BGHLV37-20_GAGTGG_L005_001.R1.fastq.gz,ETF1_BGHLV37-20_GAGTGG_L005_001.R2.fastq.gz		ENCORE2	22149