GSK3A RNA-Seq in K562

General Information


RBP	GSK3A
Cell_Line	K562
Method	CRISPR
Exp_Name	GSK3A-BGKcLV13-K562
ENCODE_series_ID	ENCSR883RLC
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR610HJO
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	GSK3A-BGKcLV13-41
Rep2	GSK3A-BGKcLV13-42
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	62.4
Rep2_qPCR	62.9
Rep1_WB	73.2
Rep2_WB	71.9
Antibody Cat#	MA3-038
Antibody Lot#	RF227934
Antibody DCC ID	ENCAB957NOP
Status	Released
Project	ENCODE4
ID	175

Experiment Information (Status: Released)

	BGKcLV13-41	BGKcLV13-42
idx	486	487
TRCN#_or_BGC#	BGC#0000323	BGC#0000323
shRNA_or_gRNA_sequence	GCCTAGAGTGGCTACGACTG	GCCTAGAGTGGCTACGACTG
PAM	tgg	tgg
Name	GSK3_85	GSK3_85
Sample_ID	BGKcLV13-41	BGKcLV13-42
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	GSK3A	GSK3A
qPCR_result	62.4	62.9
Ave_qPCR	62.7
RT-qPCR_primer-F	gagctgcagatcatgcgtaa
RT-qPCR_primer-R	gcacatattccagcaccaga
protein_conc	4865	4659
WB_result	73.2	71.9
Ave_WB	72.5
WB_DONE_date	1/4/19,2/14/19
MW	51, 47KD
IP	mouse
antibody_Cat#	MA3-038
Antibody DCC ID	NO ID
submitted_to_DCC_date	3/11/19
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4590	4591

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

	BGKcLV13-41	BGKcLV13-42
Sample_ID	BGKcLV13-41	BGKcLV13-42
Sample Name	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-42
Sample Name	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-42
RBP	GSK3A	GSK3A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2903	2904

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-41	BGKcLV13-42
Sample #	57	58
Sample Name	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-42
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-A2	1-B2
Tecan	39.55	54.64
Tecan_date	2019-03-18	2019-03-18
Size_bp	284	293
Peak_Molarity	41.20	41.80
libSampleQC_DNA_Well	DNA_Library_set42/set1/A8.png	DNA_Library_set42/set1/B8.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set42/set1/A8.png	RNA_Library_set42/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-41	BGKcLV13-42
RBP	GSK3A	GSK3A
Batch_ID	BGKcLV13	BGKcLV13
WB_result	73.200	71.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	57	58

Sequencing Information

	BGKcLV13-41	BGKcLV13-42
Sample_ID	BGKcLV13-41	BGKcLV13-42
Sample Name	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-42
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	64,183,358	59,166,404
total_aligned_reads	60,077,222	57,947,194
unique_aligned_reads	54,826,074	52,853,762
percent_uniqueAligned	0.85421	0.89331
correlation_replicates	0.996097	0.996097
spikein_reads	46,932	44,744
percent_spikeins	0.00073	0.00076
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	29	30

Data Submission Information

	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-42	BGKcLV13-42	BGKcLV13-42	BGKcLV13-42
ENCODE_alias	brenton-graveley:GSK3A-BGKcLV13	brenton-graveley:GSK3A-BGKcLV13-41	brenton-graveley:L-GSK3A-BGKcLV13-41	brenton-graveley:GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGKcLV13-K562	brenton-graveley:GSK3A-BGKcLV13-42	brenton-graveley:L-GSK3A-BGKcLV13-42	brenton-graveley:GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR610HJO	ENCBS963NIC	ENCLB937TBF	ENCFF705MYN	ENCFF079WUH	ENCSR883RLC	ENCBS701XJS	ENCLB980TTK	ENCFF406NAI	ENCFF741SMH
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	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-41	BGKcLV13-42	BGKcLV13-42	BGKcLV13-42	BGKcLV13-42
Sample Name	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-41	GSK3A-BGKcLV13-42	GSK3A-BGKcLV13-42	GSK3A-BGKcLV13-42	GSK3A-BGKcLV13-42
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-BGKcLV13-41.pdf	L-GSK3A-BGKcLV13-41.pdf				GSK3A-BGKcLV13-42.pdf	L-GSK3A-BGKcLV13-42.pdf
ID	779	853	935	979	1061	7236	854	936	980	1062

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-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	29	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	361
GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	29	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	443
GSK3A-BGKcLV13-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	29					GRCh38	V40	GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23700
GSK3A-BGKcLV13-41_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	29					GRCh38	V40	GSK3A-BGKcLV13-41/Aligned.sortedByCoord.out.bam		ENCORE2	23782
GSK3A-BGKcLV13-41_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	29					GRCh38	V40	GSK3A-BGKcLV13-41/Aligned.sortedByCoord.out.bam		ENCORE2	23864
GSK3A-BGKcLV13-41_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	29					GRCh38	V40	GSK3A-BGKcLV13-41/Aligned.sortedByCoord.out.bam		ENCORE2	23946
GSK3A-BGKcLV13-41_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	29					GRCh38	V40	GSK3A-BGKcLV13-41/Aligned.sortedByCoord.out.bam		ENCORE2	24028
GSK3A-BGKcLV13-41_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	29					GRCh38	V40	GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGKcLV13-41_TGCGGCGT+CCTCGGTA_HK3H2DSXX_S57_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24110
GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	30	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	362
GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	30	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	444
GSK3A-BGKcLV13-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	30					GRCh38	V40	GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23701
GSK3A-BGKcLV13-42_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	30					GRCh38	V40	GSK3A-BGKcLV13-42/Aligned.sortedByCoord.out.bam		ENCORE2	23783
GSK3A-BGKcLV13-42_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	30					GRCh38	V40	GSK3A-BGKcLV13-42/Aligned.sortedByCoord.out.bam		ENCORE2	23865
GSK3A-BGKcLV13-42_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	30					GRCh38	V40	GSK3A-BGKcLV13-42/Aligned.sortedByCoord.out.bam		ENCORE2	23947
GSK3A-BGKcLV13-42_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	30					GRCh38	V40	GSK3A-BGKcLV13-42/Aligned.sortedByCoord.out.bam		ENCORE2	24029
GSK3A-BGKcLV13-42_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	30					GRCh38	V40	GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R1_001.filtered.trimmed.paired.fastq.gz,GSK3A-BGKcLV13-42_CATAATAC+TTCTAACG_HK3H2DSXX_S58_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24111