YWHAG RNA-Seq in HepG2

General Information


RBP	YWHAG
Cell_Line	HepG2
Method	shRNA
Exp_Name	YWHAG-BGHLV37-HepG2
ENCODE_series_ID	ENCSR899FMX
Batch_ID	BGHLV37
Pool ID	Pool-180316
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR204QKA
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	YWHAG-BGHLV37-111C
Rep2	YWHAG-BGHLV37-112C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	81.4
Rep2_qPCR	86.2
Rep1_WB	55.5
Rep2_WB	55.8
Antibody Cat#	GTX113298
Antibody Lot#	GTX113298
Antibody DCC ID	ENCAB760OWH
Status	Released
Project	ENCODE4
ID	269

Experiment Information (Status: Released)

	BGHLV37-111	BGHLV37-112
idx	1023	1024
TRCN#_or_BGC#	TRCN0000078161	TRCN0000078161
shRNA_or_gRNA_sequence	TCTTAACTACTCCGTCTTCTA	TCTTAACTACTCCGTCTTCTA
PAM
Name	YWHAG	YWHAG
Sample_ID	BGHLV37-111	BGHLV37-112
transduction_Date	9/1/16	9/1/16
days
RBP_name	YWHAG	YWHAG
qPCR_result	81.4	86.2
Ave_qPCR	83.8
RT-qPCR_primer-F	gccatgaagaacgtgacaga
RT-qPCR_primer-R	cccccacaacgttcttgta
protein_conc	3631	3587
WB_result	55.5	55.8
Ave_WB	55.7
WB_DONE_date	9/14/16
MW	28kDa
IP	1	1
antibody_Cat#	GTX113298	GTX113298
Antibody DCC ID	ENCAB760OWH	ENCAB760OWH
submitted_to_DCC_date	10/26/16
Rep1_TPM	23.8	23.8
Rep2_TPM	28.6	28.6
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3118	3119

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

	BGHLV37-111	BGHLV37-112
Sample_ID	BGHLV37-111	BGHLV37-112
Sample Name
Sample Name	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-112C
RBP	YWHAG	YWHAG
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6449	6450

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-111	BGHLV37-112
Sample #	33	34
Sample Name	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-112C
Sample_Name_Alias
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	303	302
Peak_Molarity	31.50	39.30
libSampleQC_DNA_Well	DNA_Library_set40/set1/C7.png	DNA_Library_set40/set1/D7.png
RIN	9.0	9.2
libSample_RNA_Well	RNA_Library_set40/set1/A3.png	RNA_Library_set40/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-111	BGHLV37-112
RBP	YWHAG	YWHAG
Batch_ID	BGHLV37	BGHLV37
WB_result	55.500	55.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	956	957

Sequencing Information

	BGHLV37-111	BGHLV37-111	BGHLV37-112	BGHLV37-112
Sample_ID	BGHLV37-111	BGHLV37-111	BGHLV37-112	BGHLV37-112
Sample Name	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C
Pool ID	Pool-180109	Pool-180316	Pool-180109	Pool-180316
LocalServer_folder	set40_H	set40_H	set40_H	set40_H
total_reads	17,054,716	32,336,724	21,031,498	30,947,620
total_aligned_reads	14,853,190	28,320,354	17,508,272	25,861,598
unique_aligned_reads	14,018,258	26,727,646	16,514,638	24,394,058
percent_uniqueAligned	0.82196	0.82654	0.78523	0.78824
correlation_replicates	0.984255		0.984255
spikein_reads	7,456	14,354	5,980	8,588
percent_spikeins	0.00044	0.00044	0.00028	0.00028
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	359	401	360	402

Data Submission Information

	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112
ENCODE_alias	brenton-graveley:YWHAG-BGHLV37-C	brenton-graveley:YWHAG-BGHLV37-111C	brenton-graveley:L-YWHAG-BGHLV37-111C	brenton-graveley:YWHAG-BGHLV37-111C_GTGGCC_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:YWHAG-BGHLV37-111C_GTGGCC_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:YWHAG-BGHLV37-111C_GTGGCC_ACBYWVANXX_L003_001.R2.fastq.gz	brenton-graveley:YWHAG-BGHLV37-111C_GTGGCC_AHFKCFBCX2_L001_001.R2.fastq.gz	brenton-graveley:YWHAG-BGHLV37-HepG2	brenton-graveley:YWHAG-BGHLV37-112C	brenton-graveley:L-YWHAG-BGHLV37-112C	brenton-graveley:YWHAG-BGHLV37-112C_GTTTCG_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:YWHAG-BGHLV37-112C_GTTTCG_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:YWHAG-BGHLV37-112C_GTTTCG_ACBYWVANXX_L003_001.R2.fastq.gz	brenton-graveley:YWHAG-BGHLV37-112C_GTTTCG_AHFKCFBCX2_L001_001.R2.fastq.gz
ENCODE_accession	ENCSR204QKA	ENCBS112LZE	ENCLB251LBI	ENCFF895XLV	ENCFF673CZF	ENCFF421HAI	ENCFF808NBJ	ENCSR899FMX	ENCBS869OTH	ENCLB358ATO	ENCFF868EZZ	ENCFF661BNH	ENCFF658LQE	ENCFF632MDU
object_type	experiment	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq1	file_fastq2	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	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-111	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112	BGHLV37-112
Sample Name	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-111C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C	YWHAG-BGHLV37-112C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol						LV40_biosample_protocol	LV40_library_protocol
protocol_URL		YWHAG-BGHLV37-111C.pdf	L-YWHAG-BGHLV37-111C.pdf						YWHAG-BGHLV37-112C.pdf	L-YWHAG-BGHLV37-112C.pdf
ID	1457	1512	1568	1603	1604	1640	1641	7364	1513	1569	1605	1606	1642	1643

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
YWHAG-BGHLV37-111C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	359	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	23236
YWHAG-BGHLV37-111C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	359	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	23244
YWHAG-BGHLV37-111C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C_L001_001.R1.fastq.gz,YWHAG-BGHLV37-111C_L001_001.R2.fastq.gz		ENCORE2	23276
YWHAG-BGHLV37-111C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C/Aligned.sortedByCoord.out.bam		ENCORE2	23310
YWHAG-BGHLV37-111C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C/Aligned.sortedByCoord.out.bam		ENCORE2	23344
YWHAG-BGHLV37-111C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C/Aligned.sortedByCoord.out.bam		ENCORE2	23378
YWHAG-BGHLV37-111C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C/Aligned.sortedByCoord.out.bam		ENCORE2	23412
YWHAG-BGHLV37-111C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	359					GRCh38	V40	YWHAG-BGHLV37-111C_L001_001.R1.fastq.gz,YWHAG-BGHLV37-111C_L001_001.R2.fastq.gz		ENCORE2	23446
YWHAG-BGHLV37-112C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	360	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	23237
YWHAG-BGHLV37-112C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	360	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	23245
YWHAG-BGHLV37-112C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C_L001_001.R1.fastq.gz,YWHAG-BGHLV37-112C_L001_001.R2.fastq.gz		ENCORE2	23277
YWHAG-BGHLV37-112C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C/Aligned.sortedByCoord.out.bam		ENCORE2	23311
YWHAG-BGHLV37-112C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C/Aligned.sortedByCoord.out.bam		ENCORE2	23345
YWHAG-BGHLV37-112C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C/Aligned.sortedByCoord.out.bam		ENCORE2	23379
YWHAG-BGHLV37-112C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C/Aligned.sortedByCoord.out.bam		ENCORE2	23413
YWHAG-BGHLV37-112C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	360					GRCh38	V40	YWHAG-BGHLV37-112C_L001_001.R1.fastq.gz,YWHAG-BGHLV37-112C_L001_001.R2.fastq.gz		ENCORE2	23447