GSK3B RNA-Seq in HepG2

General Information


RBP	GSK3B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GSK3B-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR610PZO
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR426JCD
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	GSK3B-BGHcLV16-31
Rep2	GSK3B-BGHcLV16-32
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	52.5
Rep2_qPCR	53.6
Rep1_WB	54.9
Rep2_WB	61.4
Antibody Cat#	MA3-038
Antibody Lot#	RF227934
Antibody DCC ID	ENCAB957NOP
Status	Released
Project	ENCODE4
ID	151

Experiment Information (Status: Released)

	BGHcLV16-31	BGHcLV16-32
idx	461	462
TRCN#_or_BGC#	BGC#0000383	BGC#0000383
shRNA_or_gRNA_sequence	CGGCTTGCAGCTCTCCGCAA	CGGCTTGCAGCTCTCCGCAA
PAM	agg	agg
Name	GSK3B-91	GSK3B-91
Sample_ID	BGHcLV16-31	BGHcLV16-32
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	GSK3B	GSK3B
qPCR_result	52.5	53.6
Ave_qPCR	53.1
RT-qPCR_primer-F	CAAACAGACGCTCCCTGTG
RT-qPCR_primer-R	ATTCCAAAGGAATGGATATAGGCT
protein_conc	5147	4742
WB_result	54.9	61.4
Ave_WB	58.2
WB_DONE_date	5/7/19
MW	51, 47KD
IP	Mouse / Ig
antibody_Cat#	MA3-038	GSK3 alpha/beta
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	17	0
Rep2_TPM	20	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6610	6611

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

	BGHcLV16-31	BGHcLV16-32
Sample_ID	BGHcLV16-31	BGHcLV16-32
Sample Name
Sample Name	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-32
RBP	GSK3B	GSK3B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5421	5422

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-31	BGHcLV16-32
Sample #	55	56
Sample Name	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-32
Sample_Name_Alias
Index Well Position	C07	D07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-E2	1-F2
Tecan	37.14	31.03
Tecan_date	2019-12-10	2019-12-10
Size_bp	279	277
Peak_Molarity	32.60	37.50
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E2.png	DNA_Library_set43-44/set2/F2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/E7.png	RNA_Library_set43-44/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-31	BGHcLV16-32
RBP	GSK3B	GSK3B
Batch_ID	BGHcLV16	BGHcLV16
WB_result	54.900	61.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	631	632

Sequencing Information

	BGHcLV16-31	BGHcLV16-32
Sample_ID	BGHcLV16-31	BGHcLV16-32
Sample Name	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-32
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	124,083,028	106,733,370
total_aligned_reads	115,636,366	95,802,380
unique_aligned_reads	108,343,014	89,735,114
percent_uniqueAligned	0.87315	0.84074
correlation_replicates	0.998957	0.998957
spikein_reads	140,166	139,466
percent_spikeins	0.00113	0.00131
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	133	134

Data Submission Information

	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-32	BGHcLV16-32	BGHcLV16-32	BGHcLV16-32
ENCODE_alias	brenton-graveley:GSK3B-BGHcLV16	brenton-graveley:GSK3B-BGHcLV16-31	brenton-graveley:L-GSK3B-BGHcLV16-31	brenton-graveley:GSK3B-BGHcLV16-31_S51_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGHcLV16-31_S51_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGHcLV16-HepG2	brenton-graveley:GSK3B-BGHcLV16-32	brenton-graveley:L-GSK3B-BGHcLV16-32	brenton-graveley:GSK3B-BGHcLV16-32_S52_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGHcLV16-32_S52_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR426JCD	ENCBS452ZYX	ENCLB253SOU	ENCFF073JVL	ENCFF118KUA	ENCSR610PZO	ENCBS654EHE	ENCLB637DRH	ENCFF854NQW	ENCFF254IXC
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	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-31	BGHcLV16-32	BGHcLV16-32	BGHcLV16-32	BGHcLV16-32
Sample Name	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-31	GSK3B-BGHcLV16-32	GSK3B-BGHcLV16-32	GSK3B-BGHcLV16-32	GSK3B-BGHcLV16-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		GSK3B-BGHcLV16-31.pdf	L-GSK3B-BGHcLV16-31.pdf				GSK3B-BGHcLV16-32.pdf	L-GSK3B-BGHcLV16-32.pdf
ID	7	96	260	426	458	7237	97	261	427	459

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
GSK3B-BGHcLV16-31_S51_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	133	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	13
GSK3B-BGHcLV16-31_S51_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	133	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	45
GSK3B-BGHcLV16-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31_S51_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGHcLV16-31_S51_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24176
GSK3B-BGHcLV16-31_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31/Aligned.sortedByCoord.out.bam		ENCORE2	24208
GSK3B-BGHcLV16-31_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31/Aligned.sortedByCoord.out.bam		ENCORE2	24240
GSK3B-BGHcLV16-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31/Aligned.sortedByCoord.out.bam		ENCORE2	24272
GSK3B-BGHcLV16-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31/Aligned.sortedByCoord.out.bam		ENCORE2	24304
GSK3B-BGHcLV16-31_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	133					GRCh38	V40	GSK3B-BGHcLV16-31_S51_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGHcLV16-31_S51_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24336
GSK3B-BGHcLV16-32_S52_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	134	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	14
GSK3B-BGHcLV16-32_S52_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	134	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	46
GSK3B-BGHcLV16-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32_S52_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGHcLV16-32_S52_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24177
GSK3B-BGHcLV16-32_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32/Aligned.sortedByCoord.out.bam		ENCORE2	24209
GSK3B-BGHcLV16-32_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32/Aligned.sortedByCoord.out.bam		ENCORE2	24241
GSK3B-BGHcLV16-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32/Aligned.sortedByCoord.out.bam		ENCORE2	24273
GSK3B-BGHcLV16-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32/Aligned.sortedByCoord.out.bam		ENCORE2	24305
GSK3B-BGHcLV16-32_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	134					GRCh38	V40	GSK3B-BGHcLV16-32_S52_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGHcLV16-32_S52_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24337