TAF15 RNA-Seq in HepG2

General Information


RBP	TAF15
Cell_Line	HepG2
Method	shRNA
Exp_Name	TAF15-BGHLV12-HepG2
ENCODE_series_ID	ENCSR717HRT
Batch_ID	BGHLV12
Pool ID	Pool-140801
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR998RZI
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	TAF15-BGHLV12-81
Rep2	TAF15-BGHLV12-82
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	81.1
Rep2_qPCR	70.7
Rep1_WB	99.6
Rep2_WB	99.9
Antibody Cat#	A300-307A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB410IRI
Status	Released
Project	ENCODE3
ID	358

Experiment Information (Status: Released)

	BGHLV12-81	BGHLV12-81	BGHLV12-82	BGHLV12-82
idx	81	83	82	84
TRCN#_or_BGC#	TRCN0000020143	TRCN0000020143	TRCN0000020143	TRCN0000020143
shRNA_or_gRNA_sequence	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT	GCTCGAAGGAATTCCTGCAAT
PAM
Name	TAF15	TAF15	TAF15	TAF15
Sample_ID	BGHLV12-81	BGHLV12-81	BGHLV12-82	BGHLV12-82
transduction_Date	5/15/2014	5/15/2014	5/15/2014	5/15/2014
days
RBP_name	TAF15	TAF15	TAF15	TAF15
qPCR_result	81.1	81.1	70.7	70.7
Ave_qPCR	75.9	75.9
RT-qPCR_primer-F	GGGAGGCAACAGTGTCATTT	GGGAGGCAACAGTGTCATTT
RT-qPCR_primer-R	ACCTCCACTTCCACCTCCTC	ACCTCCACTTCCACCTCCTC
protein_conc	4337	4337	4454	4454
WB_result	99.6	89.1	99.9	96.8
Ave_WB	99.7	92.9
WB_DONE_date	1/22/2016	3/16/2016
MW	62kDa	62kDa	WES	WES
IP	1	1	1	1
antibody_Cat#	A300-307A	A300-308A	A300-307A	A300-308A
Antibody DCC ID		ENCAB249IHJ		ENCAB249IHJ
submitted_to_DCC_date		3/18/2016
Rep1_TPM	30.7	0	0	0
Rep2_TPM	28.2	0	0	0
Action
Library_start_date	6/12/2014		6/12/2014
repeat_library
Note
ID	2138	2140	2139	2141

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TAF15	Product_ID: A300-308A Lot_ID: 1 Source: Bethyl Labs Target Name: TAF15-human

Experiment Status

	BGHLV12-81	BGHLV12-82
Sample_ID	BGHLV12-81	BGHLV12-82
Sample Name	TAF15-BGHLV12-81	TAF15-BGHLV12-82
Sample Name	TAF15-BGHLV12-81	TAF15-BGHLV12-82
RBP	TAF15	TAF15
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	434	435

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-81	BGHLV12-82
Sample #
Sample Name	TAF15-BGHLV12-81	TAF15-BGHLV12-82
Sample_Name_Alias	TAF15-BGHLV12-81	TAF15-BGHLV12-82
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/G4.png	DNA_Library_LV12/set3/H4.png
RIN	9.4	9.2
libSample_RNA_Well	RNA_Library_LV12/set1/G8.png	RNA_Library_LV12/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-81	BGHLV12-82
RBP	TAF15	TAF15
Batch_ID	BGHLV12	BGHLV12
WB_result	99.600	99.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2058	2059

Sequencing Information

	BGHLV12-81	BGHLV12-82
Sample_ID	BGHLV12-81	BGHLV12-82
Sample Name	TAF15-BGHLV12-81	TAF15-BGHLV12-82
Pool ID	Pool-140801	Pool-140801
LocalServer_folder	set12	set12
total_reads	70,760,000	58,200,000
total_aligned_reads	65,724,366	54,461,336
unique_aligned_reads	61,790,090	51,250,716
percent_uniqueAligned	0.87323	0.88060
correlation_replicates	0.997093	0.997093
spikein_reads	301,508	277,356
percent_spikeins	0.00426	0.00477
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	758	759

Data Submission Information

	BGHLV12-81	BGHLV12-81
ENCODE_alias	brenton-graveley:TAF15-BGHLV12	brenton-graveley:TAF15-BGHLV12-HepG2
ENCODE_accession	ENCSR998RZI	ENCSR717HRT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-81	BGHLV12-81
Sample Name	TAF15-BGHLV12-81	TAF15-BGHLV12-81
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2766	6999

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
TAF15-BGHLV12-81_ATGTCA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	758	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12817
TAF15-BGHLV12-81_ATGTCA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	758	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12886
TAF15-BGHLV12-81_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81_ATGTCA_L006_R1_001.fastq.gz,TAF15-BGHLV12-81_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	12956
TAF15-BGHLV12-81_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81/Aligned.sortedByCoord.out.bam		ENCORE2	13026
TAF15-BGHLV12-81_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81/Aligned.sortedByCoord.out.bam		ENCORE2	13096
TAF15-BGHLV12-81_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81/Aligned.sortedByCoord.out.bam		ENCORE2	13166
TAF15-BGHLV12-81_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81/Aligned.sortedByCoord.out.bam		ENCORE2	13236
TAF15-BGHLV12-81_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	758					GRCh38	V40	TAF15-BGHLV12-81_ATGTCA_L006_R1_001.fastq.gz,TAF15-BGHLV12-81_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13306
TAF15-BGHLV12-82_CCGTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	759	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12818
TAF15-BGHLV12-82_CCGTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	759	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12887
TAF15-BGHLV12-82_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82_CCGTCC_L006_R1_001.fastq.gz,TAF15-BGHLV12-82_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	12957
TAF15-BGHLV12-82_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82/Aligned.sortedByCoord.out.bam		ENCORE2	13027
TAF15-BGHLV12-82_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82/Aligned.sortedByCoord.out.bam		ENCORE2	13097
TAF15-BGHLV12-82_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82/Aligned.sortedByCoord.out.bam		ENCORE2	13167
TAF15-BGHLV12-82_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82/Aligned.sortedByCoord.out.bam		ENCORE2	13237
TAF15-BGHLV12-82_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	759					GRCh38	V40	TAF15-BGHLV12-82_CCGTCC_L006_R1_001.fastq.gz,TAF15-BGHLV12-82_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13307