TRNAU1AP RNA-Seq in K562

General Information


RBP	TRNAU1AP
Cell_Line	K562
Method	CRISPR
Exp_Name	TRNAU1AP-BGKcLV06-K562
ENCODE_series_ID	ENCSR640MXX
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR889MBF
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	TRNAU1AP-BGKcLV06-39
Rep2	TRNAU1AP-BGKcLV06-40
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	20.5
Rep2_qPCR	9.0
Rep1_WB	83.7
Rep2_WB	70.6
Antibody Cat#	GTX121631
Antibody Lot#
Antibody DCC ID	ENCAB780SOA
Status	Released
Project	ENCODE3
ID	780

Experiment Information (Status: Released)

	BGKcLV06-39	BGKcLV06-40
idx	215	216
TRCN#_or_BGC#	BGC#0000068	BGC#0000068
shRNA_or_gRNA_sequence	CATTACGGTCTCCCCCATGG	CATTACGGTCTCCCCCATGG
PAM
Name	TRNAU1AP_84	TRNAU1AP_84
Sample_ID	BGKcLV06-39	BGKcLV06-40
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	TRNAU1AP	TRNAU1AP
qPCR_result	20.5	9.0
Ave_qPCR	14.8
RT-qPCR_primer-F	gtggatgatggcatgctgta
RT-qPCR_primer-R	gctcgcttctgttccagttc
protein_conc	2390	2668
WB_result	83.7	70.6
Ave_WB	77.1
WB_DONE_date	7/25/17
MW	32kd
IP
antibody_Cat#	GTX121631
Antibody DCC ID	ENCAB780SOA	ENCAB780SOA
submitted_to_DCC_date	9/29/17
Rep1_TPM	33.5	0
Rep2_TPM	30	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4313	4314

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TRNAU1AP	Product_ID: GTX121631 Lot_ID: 40863 Source: GeneTex Target Name: TRNAU1AP-human

Experiment Status

	BGKcLV06-39	BGKcLV06-40
Sample_ID	BGKcLV06-39	BGKcLV06-40
Sample Name	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-40
Sample Name	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-40
RBP	TRNAU1AP	TRNAU1AP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1377	1378

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-39	BGKcLV06-40
Sample #
Sample Name	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-40
Sample_Name_Alias	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-40
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/C3.png	DNA_Library_set39/set2/D3.png
RIN	9.4	9.9
libSample_RNA_Well	RNA_Library_set39/set3/F2.png	RNA_Library_set39/set3/G2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-39	BGKcLV06-40
RBP	TRNAU1AP	TRNAU1AP
Batch_ID	BGKcLV06	BGKcLV06
WB_result	83.700	70.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3072	3073

Sequencing Information

	BGKcLV06-39	BGKcLV06-40
Sample_ID	BGKcLV06-39	BGKcLV06-40
Sample Name	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-40
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	37,144,836	66,420,934
total_aligned_reads	32,567,900	58,885,136
unique_aligned_reads	29,713,422	53,589,574
percent_uniqueAligned	0.79993	0.80682
correlation_replicates	0.981945	0.981945
spikein_reads	16,562	23,628
percent_spikeins	0.00045	0.00036
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1723	1724

Data Submission Information

	BGKcLV06-39	BGKcLV06-39
ENCODE_alias	brenton-graveley:TRNAU1AP-BGKcLV06	brenton-graveley:TRNAU1AP-BGKcLV06-K562
ENCODE_accession	ENCSR889MBF	ENCSR640MXX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-39	BGKcLV06-39
Sample Name	TRNAU1AP-BGKcLV06-39	TRNAU1AP-BGKcLV06-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3228	7016

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
TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1723	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22492
TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1723	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22528
TRNAU1AP-BGKcLV06-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R1.fastq.gz,TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22564
TRNAU1AP-BGKcLV06-39_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39/Aligned.sortedByCoord.out.bam		ENCORE2	22600
TRNAU1AP-BGKcLV06-39_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39/Aligned.sortedByCoord.out.bam		ENCORE2	22636
TRNAU1AP-BGKcLV06-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39/Aligned.sortedByCoord.out.bam		ENCORE2	22672
TRNAU1AP-BGKcLV06-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39/Aligned.sortedByCoord.out.bam		ENCORE2	22708
TRNAU1AP-BGKcLV06-39_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1723					GRCh38	V40	TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R1.fastq.gz,TRNAU1AP-BGKcLV06-39_TTAGGC_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22744
TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1724	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22493
TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1724	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22529
TRNAU1AP-BGKcLV06-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R1.fastq.gz,TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22565
TRNAU1AP-BGKcLV06-40_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40/Aligned.sortedByCoord.out.bam		ENCORE2	22601
TRNAU1AP-BGKcLV06-40_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40/Aligned.sortedByCoord.out.bam		ENCORE2	22637
TRNAU1AP-BGKcLV06-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40/Aligned.sortedByCoord.out.bam		ENCORE2	22673
TRNAU1AP-BGKcLV06-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40/Aligned.sortedByCoord.out.bam		ENCORE2	22709
TRNAU1AP-BGKcLV06-40_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1724					GRCh38	V40	TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R1.fastq.gz,TRNAU1AP-BGKcLV06-40_TGACCA_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22745