TRA2A RNA-Seq in HepG2

General Information


RBP	TRA2A
Cell_Line	HepG2
Method	shRNA
Exp_Name	TRA2A-BGHLV14-HepG2
ENCODE_series_ID	ENCSR336TUR
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR030GZQ
ENCODE_CN_Exp_ID	ENCSR491FOC
Rep1	TRA2A_BGHLV14-61
Rep2	TRA2A_BGHLV14-62
CN1	NT_BGHLV14-1
CN2	NT_BGHLV14-2
Rep1_qPCR	91.8
Rep2_qPCR	77.8
Rep1_WB	62.6
Rep2_WB	66.3
Antibody Cat#	A303-779A
Antibody Lot#	A303-779A
Antibody DCC ID	ENCAB683DWW
Status	Released
Project	ENCODE3
ID	409

Experiment Information (Status: Released)

	BGHLV14-61	BGHLV14-62
idx	157	158
TRCN#_or_BGC#	TRCN0000074548	TRCN0000074548
shRNA_or_gRNA_sequence	CCCAATGTTATGTTATGCTTT	CCCAATGTTATGTTATGCTTT
PAM
Name	TRA2A	TRA2A
Sample_ID	BGHLV14-61	BGHLV14-62
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	TRA2A	TRA2A
qPCR_result	91.8	77.8
Ave_qPCR	84.8
RT-qPCR_primer-F	CGATCACCTTCTCCTTATTATAGTCG
RT-qPCR_primer-R	TCCTTAATTGCAACCATTCC
protein_conc	3442	3554
WB_result	62.6	66.3
Ave_WB	64.5
WB_DONE_date	5/27/2015
MW	33kDa
IP	1	1
antibody_Cat#	A303-779A	A303-779A
Antibody DCC ID	ENCAB683DWW	ENCAB683DWW
submitted_to_DCC_date	8/6/2015
Rep1_TPM	18.4	0
Rep2_TPM	15.8	0
Action
Library_start_date	8/12/2014	8/12/2014
repeat_library
Note
ID	2220	2221

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TRA2A	Product_ID: A303-779A Lot_ID: 1 Source: Bethyl Labs Target Name: TRA2A-human

Experiment Status

	BGHLV14-61	BGHLV14-62
Sample_ID	BGHLV14-61	BGHLV14-62
Sample Name	TRA2A_BGHLV14-61	TRA2A_BGHLV14-62
Sample Name	TRA2A_BGHLV14-61	TRA2A_BGHLV14-62
RBP	TRA2A	TRA2A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	542	543

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-61	BGHLV14-62
Sample #
Sample Name	TRA2A-BGHLV14-61	TRA2A-BGHLV14-62
Sample_Name_Alias	TRA2A_BGHLV14-61	TRA2A_BGHLV14-62
Index Well Position	S11	S12
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/set2/E2.png	DNA_Library_LV13-14/set2/F2.png
RIN	9.5	9.1
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/E10.png	RNA_Library_LV13-14-16/set1/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-61	BGHLV14-62
RBP	TRA2A	TRA2A
Batch_ID	BGHLV14	BGHLV14
WB_result	62.600	66.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2226	2227

Sequencing Information

	BGHLV14-61	BGHLV14-62
Sample_ID	BGHLV14-61	BGHLV14-62
Sample Name	TRA2A_BGHLV14-61	TRA2A_BGHLV14-62
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	47,540,000	45,390,000
total_aligned_reads	43,664,676	40,061,336
unique_aligned_reads	41,228,124	37,761,448
percent_uniqueAligned	0.86723	0.83193
correlation_replicates	0.994152	0.994152
spikein_reads	174,310	380,312
percent_spikeins	0.00367	0.00838
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	868	869

Data Submission Information

	BGHLV14-61	BGHLV14-61
ENCODE_alias	brenton-graveley:TRA2A_BGHLV14	brenton-graveley:TRA2A-BGHLV14-HepG2
ENCODE_accession	ENCSR030GZQ	ENCSR336TUR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-61	BGHLV14-61
Sample Name	TRA2A_BGHLV14-61	TRA2A_BGHLV14-61
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2820	7011

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
TRA2A_BGHLV14-61_GGCTAC_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	868	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13834
TRA2A_BGHLV14-61_GGCTAC_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	868	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13896
TRA2A_BGHLV14-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	868					GRCh38	V40	TRA2A_BGHLV14-61_GGCTAC_L007_R1_001.fastq.gz,TRA2A_BGHLV14-61_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	13958
TRA2A_BGHLV14-61_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	868					GRCh38	V40	TRA2A_BGHLV14-61/Aligned.sortedByCoord.out.bam		ENCORE2	14020
TRA2A_BGHLV14-61_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	868					GRCh38	V40	TRA2A_BGHLV14-61/Aligned.sortedByCoord.out.bam		ENCORE2	14082
TRA2A_BGHLV14-61_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	868					GRCh38	V40	TRA2A_BGHLV14-61/Aligned.sortedByCoord.out.bam		ENCORE2	14144
TRA2A_BGHLV14-61_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	868					GRCh38	V40	TRA2A_BGHLV14-61/Aligned.sortedByCoord.out.bam		ENCORE2	14206
TRA2A_BGHLV14-61_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	868					GRCh38	V40	TRA2A_BGHLV14-61_GGCTAC_L007_R1_001.fastq.gz,TRA2A_BGHLV14-61_GGCTAC_L007_R2_001.fastq.gz		ENCORE2	14268
TRA2A_BGHLV14-62_CTTGTA_L007_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	869	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_ATCACG_L002_R1_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R1_001.fastq.gz	ENCODE3	13835
TRA2A_BGHLV14-62_CTTGTA_L007_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	869	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_ATCACG_L002_R2_001.fastq.gz,NT_BGHLV14-2_CGATGT_L002_R2_001.fastq.gz	ENCODE3	13897
TRA2A_BGHLV14-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	869					GRCh38	V40	TRA2A_BGHLV14-62_CTTGTA_L007_R1_001.fastq.gz,TRA2A_BGHLV14-62_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	13959
TRA2A_BGHLV14-62_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	869					GRCh38	V40	TRA2A_BGHLV14-62/Aligned.sortedByCoord.out.bam		ENCORE2	14021
TRA2A_BGHLV14-62_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	869					GRCh38	V40	TRA2A_BGHLV14-62/Aligned.sortedByCoord.out.bam		ENCORE2	14083
TRA2A_BGHLV14-62_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	869					GRCh38	V40	TRA2A_BGHLV14-62/Aligned.sortedByCoord.out.bam		ENCORE2	14145
TRA2A_BGHLV14-62_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	869					GRCh38	V40	TRA2A_BGHLV14-62/Aligned.sortedByCoord.out.bam		ENCORE2	14207
TRA2A_BGHLV14-62_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	869					GRCh38	V40	TRA2A_BGHLV14-62_CTTGTA_L007_R1_001.fastq.gz,TRA2A_BGHLV14-62_CTTGTA_L007_R2_001.fastq.gz		ENCORE2	14269