GSK3B RNA-Seq in K562

General Information


RBP	GSK3B
Cell_Line	K562
Method	CRISPR
Exp_Name	GSK3B-BGKcLV15-K562
ENCODE_series_ID	ENCSR815AAE
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR025XBH
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	GSK3B-BGKcLV15-37
Rep2	GSK3B-BGKcLV15-38
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	28.9
Rep2_qPCR	32.8
Rep1_WB	72.0
Rep2_WB	65.0
Antibody Cat#	MA3-038
Antibody Lot#	RF227934
Antibody DCC ID	ENCAB957NOP
Status	Released
Project	ENCODE4
ID	128

Experiment Information (Status: Released)

	BGKcLV15-37	BGKcLV15-38
idx	575	576
TRCN#_or_BGC#	BGC#0000383	BGC#0000383
shRNA_or_gRNA_sequence	CGGCTTGCAGCTCTCCGCAA	CGGCTTGCAGCTCTCCGCAA
PAM	agg	agg
Name	GSK3A-91	GSK3A-91
Sample_ID	BGKcLV15-37	BGKcLV15-38
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	GSK3B	GSK3B
qPCR_result	28.9	32.8
Ave_qPCR	30.9
RT-qPCR_primer-F	CAAACAGACGCTCCCTGTG
RT-qPCR_primer-R	ATTCCAAAGGAATGGATATAGGCT
protein_conc	5750	5697
WB_result	72.0	65.0
Ave_WB	68.5
WB_DONE_date	4/11/19
MW	51, 47KD
IP	Mouse / Ig
antibody_Cat#	MA3-038	GSK3 alpha/beta
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	14.4	0
Rep2_TPM	13.7	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4687	4688

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

	BGKcLV15-37	BGKcLV15-38
Sample_ID	BGKcLV15-37	BGKcLV15-38
Sample Name
Sample Name	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-38
RBP	GSK3B	GSK3B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5345	5346

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-37	BGKcLV15-38
Sample #	15	16
Sample Name	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-38
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-G2	1-H2
Tecan	27.51	43.23
Tecan_date	2019-12-10	2019-12-10
Size_bp	272	269
Peak_Molarity	6.11	18.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G2.png	DNA_Library_set43-44/set1/H2.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/G2.png	RNA_Library_set43-44/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-37	BGKcLV15-38
RBP	GSK3B	GSK3B
Batch_ID	BGKcLV15	BGKcLV15
WB_result	72.000	65.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	591	592

Sequencing Information

	BGKcLV15-37	BGKcLV15-38
Sample_ID	BGKcLV15-37	BGKcLV15-38
Sample Name	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-38
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	180,206,346	109,070,444
total_aligned_reads	116,489,418	103,441,326
unique_aligned_reads	105,882,700	94,622,682
percent_uniqueAligned	0.58756	0.86754
correlation_replicates	0.990772	0.990772
spikein_reads	68,354	52,552
percent_spikeins	0.00038	0.00048
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	97	98

Data Submission Information

	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-38	BGKcLV15-38	BGKcLV15-38	BGKcLV15-38
ENCODE_alias	brenton-graveley:GSK3B-BGKcLV15	brenton-graveley:GSK3B-BGKcLV15-37	brenton-graveley:L-GSK3B-BGKcLV15-37	brenton-graveley:GSK3B-BGKcLV15-37_S15_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGKcLV15-37_S15_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGKcLV15-K562	brenton-graveley:GSK3B-BGKcLV15-38	brenton-graveley:L-GSK3B-BGKcLV15-38	brenton-graveley:GSK3B-BGKcLV15-38_S16_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3B-BGKcLV15-38_S16_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR025XBH	ENCBS665SIN	ENCLB826VFL	ENCFF805EIS	ENCFF517HJT	ENCSR815AAE	ENCBS451MGO	ENCLB427PXA	ENCFF305UXK	ENCFF676QUJ
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	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-37	BGKcLV15-38	BGKcLV15-38	BGKcLV15-38	BGKcLV15-38
Sample Name	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-37	GSK3B-BGKcLV15-38	GSK3B-BGKcLV15-38	GSK3B-BGKcLV15-38	GSK3B-BGKcLV15-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	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	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		GSK3B-BGKcLV15-37.pdf	L-ERO1L-BGKcLV15-47.pdf				GSK3B-BGKcLV15-38.pdf	L-ERO1L-BGKcLV15-48.pdf
ID	24	130	294	492	544	7238	131	295	493	545

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-BGKcLV15-37_S15_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	97	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	91
GSK3B-BGKcLV15-37_S15_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	97	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	143
GSK3B-BGKcLV15-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37_S15_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGKcLV15-37_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24382
GSK3B-BGKcLV15-37_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37/Aligned.sortedByCoord.out.bam		ENCORE2	24434
GSK3B-BGKcLV15-37_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37/Aligned.sortedByCoord.out.bam		ENCORE2	24486
GSK3B-BGKcLV15-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37/Aligned.sortedByCoord.out.bam		ENCORE2	24538
GSK3B-BGKcLV15-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37/Aligned.sortedByCoord.out.bam		ENCORE2	24590
GSK3B-BGKcLV15-37_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	97					GRCh38	V40	GSK3B-BGKcLV15-37_S15_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGKcLV15-37_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24642
GSK3B-BGKcLV15-38_S16_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	98	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	92
GSK3B-BGKcLV15-38_S16_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	98	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	144
GSK3B-BGKcLV15-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38_S16_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGKcLV15-38_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24383
GSK3B-BGKcLV15-38_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38/Aligned.sortedByCoord.out.bam		ENCORE2	24435
GSK3B-BGKcLV15-38_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38/Aligned.sortedByCoord.out.bam		ENCORE2	24487
GSK3B-BGKcLV15-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38/Aligned.sortedByCoord.out.bam		ENCORE2	24539
GSK3B-BGKcLV15-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38/Aligned.sortedByCoord.out.bam		ENCORE2	24591
GSK3B-BGKcLV15-38_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	98					GRCh38	V40	GSK3B-BGKcLV15-38_S16_R1_001.filtered.trimmed.paired.fastq.gz,GSK3B-BGKcLV15-38_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24643