GSK3A RNA-Seq in HepG2

General Information


RBP	GSK3A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GSK3A-BGHcLV14-HepG2
ENCODE_series_ID	ENCSR230NEZ
Batch_ID	BGHcLV14
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR300RMY
ENCODE_CN_Exp_ID	ENCSR750CPT
Rep1	GSK3A-BGHcLV14-41
Rep2	GSK3A-BGHcLV14-42
CN1	NT-BGHcLV14-1
CN2	NT-BGHcLV14-2
Rep1_qPCR	46.9
Rep2_qPCR	40.8
Rep1_WB	60.6
Rep2_WB	65.3
Antibody Cat#	MA3-038
Antibody Lot#
Antibody DCC ID	ENCAB957NOP
Status	Released
Project	ENCODE4
ID	174

Experiment Information (Status: Released)

	BGHcLV14-41	BGHcLV14-42
idx	396	397
TRCN#_or_BGC#	BGC#0000323	BGC#0000323
shRNA_or_gRNA_sequence	GCCTAGAGTGGCTACGACTG	GCCTAGAGTGGCTACGACTG
PAM	tgg	tgg
Name	GSK3_85	GSK3_85
Sample_ID	BGHcLV14-41	BGHcLV14-42
transduction_Date	12/5/18	12/5/18
days	D6	D6
RBP_name	GSK3A	GSK3A
qPCR_result	46.9	40.8
Ave_qPCR	43.9
RT-qPCR_primer-F	gagctgcagatcatgcgtaa
RT-qPCR_primer-R	gcacatattccagcaccaga
protein_conc	4262	3686
WB_result	60.6	65.3
Ave_WB	63.0
WB_DONE_date	1/4/19,2/15/19
MW	51, 47KD
IP	mouse
antibody_Cat#	MA3-038
Antibody DCC ID	ENCAB957NOP
submitted_to_DCC_date	3/11/19
Rep1_TPM	85	0
Rep2_TPM	70	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	6541	6542

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GSK3A	Product_ID: MA3-038 Lot_ID: RF227934 Source: Thermo Fisher Target Name: GSK3A-human

Experiment Status

	BGHcLV14-41	BGHcLV14-42
Sample_ID	BGHcLV14-41	BGHcLV14-42
Sample Name	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-42
Sample Name	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-42
RBP	GSK3A	GSK3A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2983	2984

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV14-41	BGHcLV14-42
Sample #	77	78
Sample Name	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-42
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-E2	2-F2
Tecan	74.09	53.95
Tecan_date	2019-03-18	2019-03-18
Size_bp	278	295
Peak_Molarity	69.30	50.80
libSampleQC_DNA_Well	DNA_Library_set42/set1/E10.png	DNA_Library_set42/set1/F10.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set42/set1/E10.png	RNA_Library_set42/set1/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGHcLV14-41	BGHcLV14-42
RBP	GSK3A	GSK3A
Batch_ID	BGHcLV14	BGHcLV14
WB_result	60.600	65.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	77	78

Sequencing Information

	BGHcLV14-41	BGHcLV14-42
Sample_ID	BGHcLV14-41	BGHcLV14-42
Sample Name	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-42
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	40,914,180	57,597,240
total_aligned_reads	37,376,162	53,791,748
unique_aligned_reads	35,152,372	50,639,724
percent_uniqueAligned	0.85917	0.87920
correlation_replicates	0.997490	0.997490
spikein_reads	26,710	53,688
percent_spikeins	0.00065	0.00093
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	27	28

Data Submission Information

	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-42	BGHcLV14-42	BGHcLV14-42	BGHcLV14-42
ENCODE_alias	brenton-graveley:GSK3A-BGHcLV14	brenton-graveley:GSK3A-BGHcLV14-41	brenton-graveley:L-GSK3A-BGHcLV14-41	brenton-graveley:GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGHcLV14-HepG2	brenton-graveley:GSK3A-BGHcLV14-42	brenton-graveley:L-GSK3A-BGHcLV14-42	brenton-graveley:GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR300RMY	ENCBS840EBY	ENCLB714SPW	ENCFF525TWL	ENCFF996DZC	ENCSR230NEZ	ENCBS560XUK	ENCLB125MIE	ENCFF901BLS	ENCFF220NYZ
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	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-41	BGHcLV14-42	BGHcLV14-42	BGHcLV14-42	BGHcLV14-42
Sample Name	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-41	GSK3A-BGHcLV14-42	GSK3A-BGHcLV14-42	GSK3A-BGHcLV14-42	GSK3A-BGHcLV14-42
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		GSK3A-BGHcLV14-41.pdf	L-GSK3A-BGHcLV14-41.pdf				GSK3A-BGHcLV14-42.pdf	L-GSK3A-BGHcLV14-42.pdf
ID	757	809	891	977	1059	7235	810	892	978	1060

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
GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	27	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	359
GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	27	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	441
GSK3A-BGHcLV14-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23698
GSK3A-BGHcLV14-41_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	23780
GSK3A-BGHcLV14-41_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	23862
GSK3A-BGHcLV14-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	23944
GSK3A-BGHcLV14-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41/Aligned.sortedByCoord.out.bam		ENCORE2	24026
GSK3A-BGHcLV14-41_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	27					GRCh38	V40	GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGHcLV14-41_TGCGAGAC+CATTGTTG_HK3H2DSXX_S77_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24108
GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	28	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	360
GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	28	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	442
GSK3A-BGHcLV14-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23699
GSK3A-BGHcLV14-42_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	23781
GSK3A-BGHcLV14-42_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	23863
GSK3A-BGHcLV14-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	23945
GSK3A-BGHcLV14-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42/Aligned.sortedByCoord.out.bam		ENCORE2	24027
GSK3A-BGHcLV14-42_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	28					GRCh38	V40	GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGHcLV14-42_CATAGAGT+TGCCACCA_HK3H2DSXX_S78_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24109