TARDBP RNA-Seq in HepG2

General Information


RBP	TARDBP
Cell_Line	HepG2
Method	shRNA
Exp_Name	TARDBP-BGHLV35-HepG2
ENCODE_series_ID	ENCSR627GST
Batch_ID	BGHLV35
Pool ID	Pool-160912
Local_Set_Name	set35
ENCODE_KD_Exp_ID	ENCSR527QNC
ENCODE_CN_Exp_ID	ENCSR264TUE
Rep1	TARDBP_BGHLV35-53
Rep2	TARDBP_BGHLV35-54
CN1	NT_BGHLV35-1
CN2	NT_BGHLV35-2
Rep1_qPCR	73.0
Rep2_qPCR	66.1
Rep1_WB	51.5
Rep2_WB	60.8
Antibody Cat#	A303-223A
Antibody Lot#	A303-223A
Antibody DCC ID	ENCAB057RGG
Status	Released
Project	ENCODE3
ID	741

Experiment Information (Status: Released)

	BGHLV35-53	BGHLV35-54
idx	909	910
TRCN#_or_BGC#	TRCN0000016041	TRCN0000016041
shRNA_or_gRNA_sequence	GCAATAGACAGTTAGAAAGAA	GCAATAGACAGTTAGAAAGAA
PAM
Name	TARDBP	TARDBP
Sample_ID	BGHLV35-53	BGHLV35-54
transduction_Date	4/29/16	4/29/16
days
RBP_name	TARDBP	TARDBP
qPCR_result	73.0	66.1
Ave_qPCR	69.5
RT-qPCR_primer-F	GATGGACGATGGTGTGACTG
RT-qPCR_primer-R	AGAACTCCCGCAGCTCATC
protein_conc	2590	2744
WB_result	51.5	60.8
Ave_WB	56.1
WB_DONE_date	5/23/16
MW	45kDa
IP
antibody_Cat#	A303-223A	A303-223A
Antibody DCC ID	ENCAB057RGG	ENCAB057RGG
submitted_to_DCC_date	10/26/16
Rep1_TPM	100.4	100.4
Rep2_TPM	71.3	71.3
Action
Library_start_date	07/18/16	07/18/16
repeat_library
Note
ID	3000	3001

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TARDBP	Product_ID: A303-223A Lot_ID: 1 Source: Bethyl Labs Target Name: TARDBP-human

Experiment Status

	BGHLV35-53	BGHLV35-54
Sample_ID	BGHLV35-53	BGHLV35-54
Sample Name	TARDBP_BGHLV35-53	TARDBP_BGHLV35-54
Sample Name	TARDBP_BGHLV35-53	TARDBP_BGHLV35-54
RBP	TARDBP	TARDBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1273	1274

Library-Prep
Sequencing

Library-Prep Information

	BGHLV35-53	BGHLV35-54
Sample #
Sample Name	TARDBP-BGHLV35-53	TARDBP-BGHLV35-54
Sample_Name_Alias	TARDBP_BGHLV35-53	TARDBP_BGHLV35-54
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-18	2016-07-18
Lib_ID	Lib-160718	Lib-160718
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV35/set1/C4.png	DNA_Library_LV35/set1/D4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A4.png	RNA_Library_LV35_LV36/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV35-53	BGHLV35-54
RBP	TARDBP	TARDBP
Batch_ID	BGHLV35	BGHLV35
WB_result	51.500	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2958	2959

Sequencing Information

	BGHLV35-53	BGHLV35-54
Sample_ID	BGHLV35-53	BGHLV35-54
Sample Name	TARDBP_BGHLV35-53	TARDBP_BGHLV35-54
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set35	set35
total_reads	80,541,480	82,832,280
total_aligned_reads	63,257,840	61,680,438
unique_aligned_reads	59,735,100	58,108,820
percent_uniqueAligned	0.74167	0.70152
correlation_replicates	0.999423	0.999423
spikein_reads	122,528	113,610
percent_spikeins	0.00152	0.00137
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1607	1608

Data Submission Information

	BGHLV35-53	BGHLV35-53
ENCODE_alias	brenton-graveley:TARDBP_BGHLV35	brenton-graveley:TARDBP-BGHLV35-HepG2
ENCODE_accession	ENCSR527QNC	ENCSR627GST
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV35-53	BGHLV35-53
Sample Name	TARDBP_BGHLV35-53	TARDBP_BGHLV35-53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3176	7001

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
TARDBP_BGHLV35-53_TTAGGC_L008_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1607	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21706
TARDBP_BGHLV35-53_TTAGGC_L008_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1607	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21732
TARDBP_BGHLV35-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53_TTAGGC_L008_001.R1.fastq.gz,TARDBP_BGHLV35-53_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	21758
TARDBP_BGHLV35-53_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53/Aligned.sortedByCoord.out.bam		ENCORE2	21784
TARDBP_BGHLV35-53_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53/Aligned.sortedByCoord.out.bam		ENCORE2	21810
TARDBP_BGHLV35-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53/Aligned.sortedByCoord.out.bam		ENCORE2	21836
TARDBP_BGHLV35-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53/Aligned.sortedByCoord.out.bam		ENCORE2	21862
TARDBP_BGHLV35-53_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1607					GRCh38	V40	TARDBP_BGHLV35-53_TTAGGC_L008_001.R1.fastq.gz,TARDBP_BGHLV35-53_TTAGGC_L008_001.R2.fastq.gz		ENCORE2	21888
TARDBP_BGHLV35-54_TGACCA_L008_001.R1.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1608	HiSeq2500	100	paired-ended	1				NT_BGHLV35-1_ATCACG_L005_001.R1.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R1.fastq.gz	ENCODE3	21707
TARDBP_BGHLV35-54_TGACCA_L008_001.R2.fastq.gz	ENCODE_DATA/set35/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1608	HiSeq2500	100	paired-ended	2				NT_BGHLV35-1_ATCACG_L005_001.R2.fastq.gz,NT_BGHLV35-2_CGATGT_L005_001.R2.fastq.gz	ENCODE3	21733
TARDBP_BGHLV35-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54_TGACCA_L008_001.R1.fastq.gz,TARDBP_BGHLV35-54_TGACCA_L008_001.R2.fastq.gz		ENCORE2	21759
TARDBP_BGHLV35-54_Signal.Unique.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54/Aligned.sortedByCoord.out.bam		ENCORE2	21785
TARDBP_BGHLV35-54_Signal.Unique.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54/Aligned.sortedByCoord.out.bam		ENCORE2	21811
TARDBP_BGHLV35-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54/Aligned.sortedByCoord.out.bam		ENCORE2	21837
TARDBP_BGHLV35-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set35/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54/Aligned.sortedByCoord.out.bam		ENCORE2	21863
TARDBP_BGHLV35-54_quant.sf	ENCODE_DATA/set35/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1608					GRCh38	V40	TARDBP_BGHLV35-54_TGACCA_L008_001.R1.fastq.gz,TARDBP_BGHLV35-54_TGACCA_L008_001.R2.fastq.gz		ENCORE2	21889