GTF2F1 RNA-Seq in K562

General Information


RBP	GTF2F1
Cell_Line	K562
Method	shRNA
Exp_Name	GTF2F1-BGKLV13-K562
ENCODE_series_ID	ENCSR338OYF
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR188IPO
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	GTF2F1_BGKLV13_39
Rep2	GTF2F1_BGKLV13_40
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	89.2
Rep2_qPCR	92.3
Rep1_WB	86.0
Rep2_WB	88.6
Antibody Cat#	GTX114455
Antibody Lot#	GTX114455
Antibody DCC ID	ENCAB108WPN
Status	Released
Project	ENCODE3
ID	371

Experiment Information (Status: Released)

	BGKLV13-39	BGKLV13-40
idx	174	175
TRCN#_or_BGC#	TRCN0000020836	TRCN0000020836
shRNA_or_gRNA_sequence	GCGCAAGATGATCAACGACAA	GCGCAAGATGATCAACGACAA
PAM
Name	GTF2F1	GTF2F1
Sample_ID	BGKLV13-39	BGKLV13-40
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	GTF2F1	GTF2F1
qPCR_result	89.2	92.3
Ave_qPCR	90.7
RT-qPCR_primer-F	caccatcaggcaagacaaca
RT-qPCR_primer-R	ccttagtggtcatgggcttc
protein_conc	2179	2271
WB_result	86.0	88.6
Ave_WB	87.3
WB_DONE_date	6/10/2015
MW	58kDa
IP	1	1
antibody_Cat#	GTX114455	GTX114455
Antibody DCC ID	ENCAB108WPN	ENCAB108WPN
submitted_to_DCC_date	8/6/2015
Rep1_TPM	49.8546441	0
Rep2_TPM	75.4395376	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	193	194

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-39	BGKLV13-40
Sample_ID	BGKLV13-39	BGKLV13-40
Sample Name	GTF2F1_BGKLV13_39	GTF2F1_BGKLV13_40
Sample Name	GTF2F1_BGKLV13_39	GTF2F1_BGKLV13_40
RBP	GTF2F1	GTF2F1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	454	455

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-39	BGKLV13-40
Sample #
Sample Name	GTF2F1-BGKLV13-39	GTF2F1-BGKLV13-40
Sample_Name_Alias	GTF2F1_BGKLV13_39	GTF2F1_BGKLV13_40
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/B4.png	DNA_Library_LV13-14/set1/C4.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV12/set1/E12.png	RNA_Library_LV12/set1/F12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-39	BGKLV13-40
RBP	GTF2F1	GTF2F1
Batch_ID	BGKLV13	BGKLV13
WB_result	86.000	88.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2144	2145

Sequencing Information

	BGKLV13-39	BGKLV13-40
Sample_ID	BGKLV13-39	BGKLV13-40
Sample Name	GTF2F1_BGKLV13_39	GTF2F1_BGKLV13_40
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	50,920,000	45,750,000
total_aligned_reads	47,698,990	42,396,638
unique_aligned_reads	43,998,484	38,892,636
percent_uniqueAligned	0.86407	0.85011
correlation_replicates	0.984422	0.984422
spikein_reads	207,528	293,540
percent_spikeins	0.00408	0.00642
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	786	787

Data Submission Information

	BGKLV13-39	BGKLV13-39
ENCODE_alias	brenton-graveley:GTF2F1_BGKLV13	brenton-graveley:GTF2F1-BGKLV13-K562
ENCODE_accession	ENCSR188IPO	ENCSR338OYF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-39	BGKLV13-39
Sample Name	GTF2F1_BGKLV13_39	GTF2F1_BGKLV13_39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2776	6742

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_BGKLV13_39_ATCACG_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	786	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13382
GTF2F1_BGKLV13_39_ATCACG_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	786	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13434
GTF2F1_BGKLV13_39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39_ATCACG_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_39_ATCACG_L004_R2_001.fastq.gz		ENCORE2	13486
GTF2F1_BGKLV13_39_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39/Aligned.sortedByCoord.out.bam		ENCORE2	13538
GTF2F1_BGKLV13_39_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39/Aligned.sortedByCoord.out.bam		ENCORE2	13590
GTF2F1_BGKLV13_39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39/Aligned.sortedByCoord.out.bam		ENCORE2	13642
GTF2F1_BGKLV13_39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39/Aligned.sortedByCoord.out.bam		ENCORE2	13694
GTF2F1_BGKLV13_39_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	786					GRCh38	V40	GTF2F1_BGKLV13_39_ATCACG_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_39_ATCACG_L004_R2_001.fastq.gz		ENCORE2	13746
GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	787	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13383
GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	787	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13435
GTF2F1_BGKLV13_40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gz		ENCORE2	13487
GTF2F1_BGKLV13_40_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bam		ENCORE2	13539
GTF2F1_BGKLV13_40_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bam		ENCORE2	13591
GTF2F1_BGKLV13_40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bam		ENCORE2	13643
GTF2F1_BGKLV13_40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40/Aligned.sortedByCoord.out.bam		ENCORE2	13695
GTF2F1_BGKLV13_40_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	787					GRCh38	V40	GTF2F1_BGKLV13_40_CGATGT_L004_R1_001.fastq.gz,GTF2F1_BGKLV13_40_CGATGT_L004_R2_001.fastq.gz		ENCORE2	13747