YWHAG RNA-Seq in K562

General Information


RBP	YWHAG
Cell_Line	K562
Method	CRISPR
Exp_Name	YWHAG-BGKcLV08-K562
ENCODE_series_ID	ENCSR135BEX
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR163PNO
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	YWHAG-BGKcLV08-79
Rep2	YWHAG-BGKcLV08-80
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	49.2
Rep2_qPCR	62.6
Rep1_WB	63.0
Rep2_WB	67.5
Antibody Cat#	GTX113298
Antibody Lot#	GTX113298
Antibody DCC ID	ENCAB760OWH
Status	Released
Project	ENCODE4
ID	212

Experiment Information (Status: Released)

	BGKcLV08-79	BGKcLV08-80
idx	304	305
TRCN#_or_BGC#	BGC#0000160	BGC#0000160
shRNA_or_gRNA_sequence	GAGCCAGGCCTAATCGGATG	GAGCCAGGCCTAATCGGATG
PAM	GGG	GGG
Name	YWHAG-91F	YWHAG-91F
Sample_ID	BGKcLV08-79	BGKcLV08-80
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	YWHAG	YWHAG
qPCR_result	49.2	62.6
Ave_qPCR	55.9
RT-qPCR_primer-F	gccatgaagaacgtgacaga
RT-qPCR_primer-R	cccccacaacgttcttgta
protein_conc	3104	3620
WB_result	63.0	67.5
Ave_WB	65.2
WB_DONE_date	3/27/18
MW	28kDa
IP	1	1
antibody_Cat#	GTX113298	GTX113298
Antibody DCC ID	ENCAB760OWH
submitted_to_DCC_date	9/6/18
Rep1_TPM	99.6	0
Rep2_TPM	69.6	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4404	4405

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YWHAG	Product_ID: GTX113298 Lot_ID: 40128 Source: GeneTex Target Name: YWHAG-human

Experiment Status

	BGKcLV08-79	BGKcLV08-80
Sample_ID	BGKcLV08-79	BGKcLV08-80
Sample Name
Sample Name	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-80
RBP	YWHAG	YWHAG
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6195	6196

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-79	BGKcLV08-80
Sample #	31	32
Sample Name	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-80
Sample_Name_Alias
Index Well Position	G04	H04
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	278	281
Peak_Molarity	76.70	46.30
libSampleQC_DNA_Well	DNA_Library_set41/set2/G4.png	DNA_Library_set41/set2/H4.png
RIN	9.2	9.9
libSample_RNA_Well	RNA_Library_set41/set1/G4.png	RNA_Library_set41/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-27	2018-07-27
Sample_ID	BGKcLV08-79	BGKcLV08-80
RBP	YWHAG	YWHAG
Batch_ID	BGKcLV08	BGKcLV08
WB_result	63.000	67.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	881	882

Sequencing Information

	BGKcLV08-79	BGKcLV08-80
Sample_ID	BGKcLV08-79	BGKcLV08-80
Sample Name	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-80
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	171,117,078	59,302,242
total_aligned_reads	167,127,138	58,425,232
unique_aligned_reads	150,680,592	52,771,934
percent_uniqueAligned	0.88057	0.88988
correlation_replicates	0.997155	0.997155
spikein_reads	281,380	112,602
percent_spikeins	0.00164	0.00190
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	287	288

Data Submission Information

	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-80	BGKcLV08-80	BGKcLV08-80	BGKcLV08-80
ENCODE_alias	brenton-graveley:YWHAG-BGKcLV08	brenton-graveley:YWHAG-BGKcLV08-79	brenton-graveley:L-YWHAG-BGKcLV08-79	brenton-graveley:YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YWHAG-BGKcLV08-K562	brenton-graveley:YWHAG-BGKcLV08-80	brenton-graveley:L-YWHAG-BGKcLV08-80	brenton-graveley:YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR163PNO	ENCBS587LTT	ENCLB333ZJF	ENCFF660EBB	ENCFF414KLY	ENCSR135BEX	ENCBS969ZSB	ENCLB929OGL	ENCFF292YWP	ENCFF290FRG
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	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-79	BGKcLV08-80	BGKcLV08-80	BGKcLV08-80	BGKcLV08-80
Sample Name	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-79	YWHAG-BGKcLV08-80	YWHAG-BGKcLV08-80	YWHAG-BGKcLV08-80	YWHAG-BGKcLV08-80
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		YWHAG-BGKcLV08-79.pdf	L-YWHAG-BGKcLV08-79.pdf				YWHAG-BGKcLV08-80.pdf	L-YWHAG-BGKcLV08-80.pdf
ID	1146	1212	1282	1352	1416	7365	1213	1283	1353	1417

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
YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	287				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	559
YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	287				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	629
YWHAG-BGKcLV08-79_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	287	GRCh38	V40	YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26797
YWHAG-BGKcLV08-79_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	287	GRCh38	V40	YWHAG-BGKcLV08-79/Aligned.sortedByCoord.out.bam		ENCORE2	26867
YWHAG-BGKcLV08-79_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	287	GRCh38	V40	YWHAG-BGKcLV08-79/Aligned.sortedByCoord.out.bam		ENCORE2	26937
YWHAG-BGKcLV08-79_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	287	GRCh38	V40	YWHAG-BGKcLV08-79/Aligned.sortedByCoord.out.bam		ENCORE2	27007
YWHAG-BGKcLV08-79_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	287	GRCh38	V40	YWHAG-BGKcLV08-79/Aligned.sortedByCoord.out.bam		ENCORE2	27077
YWHAG-BGKcLV08-79_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	287	GRCh38	V40	YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BGKcLV08-79_GGCATTCT+CTAGCTTG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27147
YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	288				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	560
YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	288				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	630
YWHAG-BGKcLV08-80_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	288	GRCh38	V40	YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26798
YWHAG-BGKcLV08-80_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	288	GRCh38	V40	YWHAG-BGKcLV08-80/Aligned.sortedByCoord.out.bam		ENCORE2	26868
YWHAG-BGKcLV08-80_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	288	GRCh38	V40	YWHAG-BGKcLV08-80/Aligned.sortedByCoord.out.bam		ENCORE2	26938
YWHAG-BGKcLV08-80_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	288	GRCh38	V40	YWHAG-BGKcLV08-80/Aligned.sortedByCoord.out.bam		ENCORE2	27008
YWHAG-BGKcLV08-80_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	288	GRCh38	V40	YWHAG-BGKcLV08-80/Aligned.sortedByCoord.out.bam		ENCORE2	27078
YWHAG-BGKcLV08-80_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	288	GRCh38	V40	YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BGKcLV08-80_AATGCCTC+TCGATCCA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27148