TRNAU1AP RNA-Seq in HepG2

General Information


RBP	TRNAU1AP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	TRNAU1AP-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR522VAZ
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR481AIB
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	TRNAU1AP-BGHcLV10-51
Rep2	TRNAU1AP-BGHcLV10-52
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	54.8
Rep2_qPCR	45.4
Rep1_WB	58.6
Rep2_WB	53.2
Antibody Cat#	GTX121631
Antibody Lot#
Antibody DCC ID	ENCAB780SOA
Status	Released
Project	ENCODE4
ID	227

Experiment Information (Status: Released)

	BGHcLV10-51	BGHcLV10-52
idx	248	249
TRCN#_or_BGC#	BGC#0000239	BGC#0000239
shRNA_or_gRNA_sequence	CATGCCATCATCCACGTCCG	CATGCCATCATCCACGTCCG
PAM	GGG	GGG
Name	TRNAU1AP	TRNAU1AP
Sample_ID	BGHcLV10-51	BGHcLV10-52
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	TRNAU1AP	TRNAU1AP
qPCR_result	54.8	45.4
Ave_qPCR	50.1
RT-qPCR_primer-F	gtggatgatggcatgctgta
RT-qPCR_primer-R	gctcgcttctgttccagttc
protein_conc	2886	3597
WB_result	58.6	53.2
Ave_WB	55.9
WB_DONE_date	5/7/18
MW	32kd
IP
antibody_Cat#	GTX121631
Antibody DCC ID	ENCAB780SOA
submitted_to_DCC_date	9/6/18
Rep1_TPM	16	0
Rep2_TPM	21	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6391	6392

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

	BGHcLV10-51	BGHcLV10-52
Sample_ID	BGHcLV10-51	BGHcLV10-52
Sample Name
Sample Name	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-52
RBP	TRNAU1AP	TRNAU1AP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6305	6306

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-51	BGHcLV10-52
Sample #	65	66
Sample Name	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-52
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	281	282
Peak_Molarity	42.80	42.30
libSampleQC_DNA_Well	DNA_Library_set41/set5/E9.png	DNA_Library_set41/set5/F9.png
RIN	9.4	9.8
libSample_RNA_Well	RNA_Library_set41/set1/A9.png	RNA_Library_set41/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-51	BGHcLV10-52
RBP	TRNAU1AP	TRNAU1AP
Batch_ID	BGHcLV10	BGHcLV10
WB_result	58.600	53.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	915	916

Sequencing Information

	BGHcLV10-51	BGHcLV10-52
Sample_ID	BGHcLV10-51	BGHcLV10-52
Sample Name	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-52
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	157,647,148	106,180,608
total_aligned_reads	148,637,870	99,707,046
unique_aligned_reads	138,594,792	93,024,508
percent_uniqueAligned	0.87915	0.87610
correlation_replicates	0.992438	0.992438
spikein_reads	343,834	220,862
percent_spikeins	0.00218	0.00208
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	321	322

Data Submission Information

	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-52	BGHcLV10-52	BGHcLV10-52	BGHcLV10-52
ENCODE_alias	brenton-graveley:TRNAU1AP-BGHcLV10	brenton-graveley:TRNAU1AP-BGHcLV10-51	brenton-graveley:L-TRNAU1AP-BGHcLV10-51	brenton-graveley:TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRNAU1AP-BGHcLV10-HepG2	brenton-graveley:TRNAU1AP-BGHcLV10-52	brenton-graveley:L-TRNAU1AP-BGHcLV10-52	brenton-graveley:TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR481AIB	ENCBS210ZHC	ENCLB402LJS	ENCFF961FEM	ENCFF167AXN	ENCSR522VAZ	ENCBS558FIL	ENCLB040VNF	ENCFF411QQL	ENCFF544TWW
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-51	BGHcLV10-52	BGHcLV10-52	BGHcLV10-52	BGHcLV10-52
Sample Name	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-51	TRNAU1AP-BGHcLV10-52	TRNAU1AP-BGHcLV10-52	TRNAU1AP-BGHcLV10-52	TRNAU1AP-BGHcLV10-52
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		TRNAU1AP-BGHcLV10-51.pdf	L-TRNAU1AP-BGHcLV10-51.pdf				TRNAU1AP-BGHcLV10-52.pdf	L-TRNAU1AP-BGHcLV10-52.pdf
ID	1145	1210	1280	1350	1414	7348	1211	1281	1351	1415

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	321				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	557
TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	321				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	627
TRNAU1AP-BGHcLV10-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26795
TRNAU1AP-BGHcLV10-51_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51/Aligned.sortedByCoord.out.bam		ENCORE2	26865
TRNAU1AP-BGHcLV10-51_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51/Aligned.sortedByCoord.out.bam		ENCORE2	26935
TRNAU1AP-BGHcLV10-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51/Aligned.sortedByCoord.out.bam		ENCORE2	27005
TRNAU1AP-BGHcLV10-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51/Aligned.sortedByCoord.out.bam		ENCORE2	27075
TRNAU1AP-BGHcLV10-51_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	321	GRCh38	V40	TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BGHcLV10-51_GCCACAGG+CATGCCAT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27145
TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	322				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	558
TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	322				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	628
TRNAU1AP-BGHcLV10-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26796
TRNAU1AP-BGHcLV10-52_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52/Aligned.sortedByCoord.out.bam		ENCORE2	26866
TRNAU1AP-BGHcLV10-52_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52/Aligned.sortedByCoord.out.bam		ENCORE2	26936
TRNAU1AP-BGHcLV10-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52/Aligned.sortedByCoord.out.bam		ENCORE2	27006
TRNAU1AP-BGHcLV10-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52/Aligned.sortedByCoord.out.bam		ENCORE2	27076
TRNAU1AP-BGHcLV10-52_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	322	GRCh38	V40	TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,TRNAU1AP-BGHcLV10-52_ATTGTGAA+TGCATTGC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27146