GTF2F1 RNA-Seq in HepG2

General Information


RBP	GTF2F1
Cell_Line	HepG2
Method	shRNA
Exp_Name	GTF2F1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR353CDH
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR295XKC
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	GTF2F1_BGHLV14-23
Rep2	GTF2F1_BGHLV14-24
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	71.5
Rep2_qPCR	71.5
Rep1_WB	90.3
Rep2_WB	85.4
Antibody Cat#	GTX114455
Antibody Lot#	GTX114455
Antibody DCC ID	ENCAB108WPN
Status	Released
Project	ENCODE3
ID	394

Experiment Information (Status: Released)

	BGHLV14-23	BGHLV14-23	BGHLV14-24	BGHLV14-24
idx	119	0	120	0
TRCN#_or_BGC#	TRCN0000020836	TRCN0000020836	TRCN0000020836	TRCN0000020836
shRNA_or_gRNA_sequence	GCGCAAGATGATCAACGACAA	GCGCAAGATGATCAACGACAA	GCGCAAGATGATCAACGACAA	GCGCAAGATGATCAACGACAA
PAM
Name	GTF2F1/TFIIF	GTF2F1/TFIIF	GTF2F1/TFIIF	GTF2F1/TFIIF
Sample_ID	BGHLV14-23	BGHLV14-23	BGHLV14-24	BGHLV14-24
transduction_Date	7/4/2014	7/4/2014	7/4/2014	7/4/2014
days
RBP_name	GTF2F1	GTF2F1	GTF2F1	GTF2F1
qPCR_result	71.5	71.5	71.5	71.5
Ave_qPCR	71.5	71.5
RT-qPCR_primer-F	caccatcaggcaagacaaca	caccatcaggcaagacaaca
RT-qPCR_primer-R	ccttagtggtcatgggcttc	ccttagtggtcatgggcttc
protein_conc	4199	4199	4190	4190
WB_result	90.3	87.0	85.4	96.9
Ave_WB	87.9	91.9
WB_DONE_date	5/27/2015	6/12/2019
MW	58kDa	58kDa
IP	1		1
antibody_Cat#	GTX114455	PA5-30050	GTX114455
Antibody DCC ID	ENCAB108WPN	ENCAB576INM	ENCAB108WPN	LOT# TL2692997A
submitted_to_DCC_date	8/6/2015
Rep1_TPM	27.9	0	0	0
Rep2_TPM	33.7	0	0	0
Action
Library_start_date	8/12/2014		8/12/2014
repeat_library
Note
ID	2176	2178	2177	2179

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GTF2F1	Product_ID: GTX114455 Lot_ID: 40723 Source: GeneTex Target Name: GTF2F1-human
GTF2F1	Product_ID: PA5-30050 Lot_ID: TL2692997A Source: Thermo Fisher Target Name: GTF2F1-human

Experiment Status

	BGHLV14-23	BGHLV14-24
Sample_ID	BGHLV14-23	BGHLV14-24
Sample Name	GTF2F1_BGHLV14-23	GTF2F1_BGHLV14-24
Sample Name	GTF2F1_BGHLV14-23	GTF2F1_BGHLV14-24
RBP	GTF2F1	GTF2F1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	510	511

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-23	BGHLV14-24
Sample #
Sample Name	GTF2F1-BGHLV14-23	GTF2F1-BGHLV14-24
Sample_Name_Alias	GTF2F1_BGHLV14-23	GTF2F1_BGHLV14-24
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-08-12	2014-08-12
Lib_ID	Lib-140812	Lib-140812
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F10.png	DNA_Library_LV13-14/set1/G10.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G6.png	RNA_Library_LV13-14-16/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-23	BGHLV14-24
RBP	GTF2F1	GTF2F1
Batch_ID	BGHLV14	BGHLV14
WB_result	90.300	85.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2196	2197

Sequencing Information

	BGHLV14-23	BGHLV14-24
Sample_ID	BGHLV14-23	BGHLV14-24
Sample Name	GTF2F1_BGHLV14-23	GTF2F1_BGHLV14-24
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	49,990,000	54,270,000
total_aligned_reads	45,237,236	49,447,932
unique_aligned_reads	42,677,780	46,733,192
percent_uniqueAligned	0.85373	0.86112
correlation_replicates	0.998484	0.998484
spikein_reads	365,426	313,370
percent_spikeins	0.00731	0.00577
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	838	839

Data Submission Information

	BGHLV14-23	BGHLV14-23
ENCODE_alias	brenton-graveley:GTF2F1_BGHLV14	brenton-graveley:GTF2F1-BGHLV14-HepG2
ENCODE_accession	ENCSR295XKC	ENCSR353CDH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-23	BGHLV14-23
Sample Name	GTF2F1_BGHLV14-23	GTF2F1_BGHLV14-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2805	6741

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
GTF2F1_BGHLV14-23_ACAGTG_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	838	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13802
GTF2F1_BGHLV14-23_ACAGTG_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	838	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13864
GTF2F1_BGHLV14-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23_ACAGTG_L003_R1_001.fastq.gz,GTF2F1_BGHLV14-23_ACAGTG_L003_R2_001.fastq.gz		ENCORE2	13926
GTF2F1_BGHLV14-23_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23/Aligned.sortedByCoord.out.bam		ENCORE2	13988
GTF2F1_BGHLV14-23_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23/Aligned.sortedByCoord.out.bam		ENCORE2	14050
GTF2F1_BGHLV14-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23/Aligned.sortedByCoord.out.bam		ENCORE2	14112
GTF2F1_BGHLV14-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23/Aligned.sortedByCoord.out.bam		ENCORE2	14174
GTF2F1_BGHLV14-23_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	838					GRCh38	V40	GTF2F1_BGHLV14-23_ACAGTG_L003_R1_001.fastq.gz,GTF2F1_BGHLV14-23_ACAGTG_L003_R2_001.fastq.gz		ENCORE2	14236
GTF2F1_BGHLV14-24_GCCAAT_L003_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	839	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13803
GTF2F1_BGHLV14-24_GCCAAT_L003_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	839	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13865
GTF2F1_BGHLV14-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24_GCCAAT_L003_R1_001.fastq.gz,GTF2F1_BGHLV14-24_GCCAAT_L003_R2_001.fastq.gz		ENCORE2	13927
GTF2F1_BGHLV14-24_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24/Aligned.sortedByCoord.out.bam		ENCORE2	13989
GTF2F1_BGHLV14-24_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24/Aligned.sortedByCoord.out.bam		ENCORE2	14051
GTF2F1_BGHLV14-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24/Aligned.sortedByCoord.out.bam		ENCORE2	14113
GTF2F1_BGHLV14-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24/Aligned.sortedByCoord.out.bam		ENCORE2	14175
GTF2F1_BGHLV14-24_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	839					GRCh38	V40	GTF2F1_BGHLV14-24_GCCAAT_L003_R1_001.fastq.gz,GTF2F1_BGHLV14-24_GCCAAT_L003_R2_001.fastq.gz		ENCORE2	14237