TFIP11 RNA-Seq in HepG2

General Information


RBP	TFIP11
Cell_Line	HepG2
Method	shRNA
Exp_Name	TFIP11-BGHLV17-HepG2
ENCODE_series_ID	ENCSR584CON
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR573UBF
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	TFIP11_BGHLV17_33
Rep2	TFIP11_BGHLV17_34
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	68.2
Rep2_qPCR	67.5
Rep1_WB	97.1
Rep2_WB	99.6
Antibody Cat#	A302-548A
Antibody Lot#	A302-548A
Antibody DCC ID	ENCAB593XBQ
Status	Released
Project	ENCODE3
ID	440

Experiment Information (Status: Released)

	BGHLV17-33	BGHLV17-34
idx	269	270
TRCN#_or_BGC#	TRCN0000074507	TRCN0000074507
shRNA_or_gRNA_sequence	CCTGGGTTGGAAGTCGATGTT	CCTGGGTTGGAAGTCGATGTT
PAM
Name	TFIP11	TFIP11
Sample_ID	BGHLV17-33	BGHLV17-34
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	TFIP11	TFIP11
qPCR_result	68.2	67.5
Ave_qPCR	67.9
RT-qPCR_primer-F	gcacatccatctgtcaagga
RT-qPCR_primer-R	tgtgggtgagataggcaatg
protein_conc	2158	2119
WB_result	97.1	99.6
Ave_WB	98.4
WB_DONE_date	4/17/2015
MW	97kDa
IP	1	1
antibody_Cat#	A302-548A	A302-548A
Antibody DCC ID	ENCAB593XBQ	ENCAB593XBQ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	5.4	0
Rep2_TPM	8.7	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2334	2335

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TFIP11	Product_ID: A302-548A Lot_ID: 1 Source: Bethyl Labs Target Name: TFIP11-human

Experiment Status

	BGHLV17-33	BGHLV17-34
Sample_ID	BGHLV17-33	BGHLV17-34
Sample Name	TFIP11_BGHLV17_33	TFIP11_BGHLV17_34
Sample Name	TFIP11_BGHLV17_33	TFIP11_BGHLV17_34
RBP	TFIP11	TFIP11
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	608	609

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-33	BGHLV17-34
Sample #
Sample Name	TFIP11-BGHLV17-33	TFIP11-BGHLV17-34
Sample_Name_Alias	TFIP11_BGHLV17_33	TFIP11_BGHLV17_34
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E3.png	DNA_Library_LV16-17/set1/F3.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E5.png	RNA_Library_LV16-17-18/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-33	BGHLV17-34
RBP	TFIP11	TFIP11
Batch_ID	BGHLV17	BGHLV17
WB_result	97.100	99.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2292	2293

Sequencing Information

	BGHLV17-33	BGHLV17-34
Sample_ID	BGHLV17-33	BGHLV17-34
Sample Name	TFIP11_BGHLV17_33	TFIP11_BGHLV17_34
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	51,260,000	22,730,000
total_aligned_reads	46,016,726	20,079,226
unique_aligned_reads	43,563,666	19,012,962
percent_uniqueAligned	0.84986	0.83647
correlation_replicates	0.998028	0.998028
spikein_reads	461,344	72,778
percent_spikeins	0.00900	0.00320
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	934	935

Data Submission Information

	BGHLV17-33	BGHLV17-33
ENCODE_alias	brenton-graveley:TFIP11_BGHLV17	brenton-graveley:TFIP11-BGHLV17-HepG2
ENCODE_accession	ENCSR573UBF	ENCSR584CON
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-33	BGHLV17-33
Sample Name	TFIP11_BGHLV17_33	TFIP11_BGHLV17_33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2871	7005

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
TFIP11_BGHLV17_33_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	934	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14516
TFIP11_BGHLV17_33_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	934	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14554
TFIP11_BGHLV17_33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33_CGTACG_L003_R1_001.fastq.gz,TFIP11_BGHLV17_33_CGTACG_L003_R2_001.fastq.gz		ENCORE2	14592
TFIP11_BGHLV17_33_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33/Aligned.sortedByCoord.out.bam		ENCORE2	14630
TFIP11_BGHLV17_33_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33/Aligned.sortedByCoord.out.bam		ENCORE2	14668
TFIP11_BGHLV17_33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33/Aligned.sortedByCoord.out.bam		ENCORE2	14706
TFIP11_BGHLV17_33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33/Aligned.sortedByCoord.out.bam		ENCORE2	14744
TFIP11_BGHLV17_33_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	934					GRCh38	V40	TFIP11_BGHLV17_33_CGTACG_L003_R1_001.fastq.gz,TFIP11_BGHLV17_33_CGTACG_L003_R2_001.fastq.gz		ENCORE2	14782
TFIP11_BGHLV17_34_GAGTGG_L003_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	935	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14517
TFIP11_BGHLV17_34_GAGTGG_L003_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	935	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14555
TFIP11_BGHLV17_34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34_GAGTGG_L003_R1_001.fastq.gz,TFIP11_BGHLV17_34_GAGTGG_L003_R2_001.fastq.gz		ENCORE2	14593
TFIP11_BGHLV17_34_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34/Aligned.sortedByCoord.out.bam		ENCORE2	14631
TFIP11_BGHLV17_34_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34/Aligned.sortedByCoord.out.bam		ENCORE2	14669
TFIP11_BGHLV17_34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34/Aligned.sortedByCoord.out.bam		ENCORE2	14707
TFIP11_BGHLV17_34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34/Aligned.sortedByCoord.out.bam		ENCORE2	14745
TFIP11_BGHLV17_34_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	935					GRCh38	V40	TFIP11_BGHLV17_34_GAGTGG_L003_R1_001.fastq.gz,TFIP11_BGHLV17_34_GAGTGG_L003_R2_001.fastq.gz		ENCORE2	14783