GNL3 RNA-Seq in K562

General Information


RBP	GNL3
Cell_Line	K562
Method	CRISPR
Exp_Name	GNL3-BGKcLV08-K562
ENCODE_series_ID	ENCSR591RYB
Batch_ID	BGKcLV08
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR455VFL
ENCODE_CN_Exp_ID	ENCSR015KGT
Rep1	GNL3-BGKcLV08-93
Rep2	GNL3-BGKcLV08-94
CN1	NT-BGKcLV08-1
CN2	NT-BGKcLV08-2
Rep1_qPCR	27.5
Rep2_qPCR	13.0
Rep1_WB	90.8
Rep2_WB	96.9
Antibody Cat#	A300-599A
Antibody Lot#	A300-599A
Antibody DCC ID	ENCAB664GBP
Status	Released
Project	ENCODE4
ID	214

Experiment Information (Status: Released)

	BGKcLV08-93	BGKcLV08-94
idx	314	315
TRCN#_or_BGC#	BGC#0000038	BGC#0000038
shRNA_or_gRNA_sequence	CACCTCTAGGACAACATCGG	CACCTCTAGGACAACATCGG
PAM
Name	GNL3_6-F	GNL3_6-F
Sample_ID	BGKcLV08-93	BGKcLV08-94
transduction_Date	3/8/18	3/8/18
days	Day 6	Day 6
RBP_name	GNL3	GNL3
qPCR_result	27.5	13.0
Ave_qPCR	20.3
RT-qPCR_primer-F	cccaggagttccaaacagtg
RT-qPCR_primer-R	tgcctgtcaagtttctgctg
protein_conc	3070	2533
WB_result	90.8	96.9
Ave_WB	93.8
WB_DONE_date	3/15/18	WES
MW	62 kDa
IP	1
antibody_Cat#	A300-599A	A300-599A
Antibody DCC ID	ENCAB664GBP
submitted_to_DCC_date	9/6/18
Rep1_TPM	163.3	0
Rep2_TPM	70.7	0
Action	Ready	Ready
Library_start_date	7/26/18	7/26/18
repeat_library
Note
ID	4414	4415

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GNL3	Product_ID: A300-599A Lot_ID: 1 Source: Bethyl Labs Target Name: GNL3-human

Experiment Status

	BGKcLV08-93	BGKcLV08-94
Sample_ID	BGKcLV08-93	BGKcLV08-94
Sample Name
Sample Name	GNL3-BGKcLV08-93	GNL3-BGKcLV08-94
RBP	GNL3	GNL3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6199	6200

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV08-93	BGKcLV08-94
Sample #	35	36
Sample Name	GNL3-BGKcLV08-93	GNL3-BGKcLV08-94
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	273	278
Peak_Molarity	213.00	65.60
libSampleQC_DNA_Well	DNA_Library_set41/set3/B1.png	DNA_Library_set41/set2/D5.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set41/set1/C5.png	RNA_Library_set41/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-07-31	2018-07-31
Sample_ID	BGKcLV08-93	BGKcLV08-94
RBP	GNL3	GNL3
Batch_ID	BGKcLV08	BGKcLV08
WB_result	90.800	96.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	885	886

Sequencing Information

	BGKcLV08-93	BGKcLV08-94
Sample_ID	BGKcLV08-93	BGKcLV08-94
Sample Name	GNL3-BGKcLV08-93	GNL3-BGKcLV08-94
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	119,017,426	131,676,190
total_aligned_reads	116,319,872	125,849,570
unique_aligned_reads	104,368,664	112,363,000
percent_uniqueAligned	0.87692	0.85333
correlation_replicates	0.992103	0.992103
spikein_reads	164,576	176,728
percent_spikeins	0.00138	0.00134
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	291	292

Data Submission Information

	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-94	BGKcLV08-94	BGKcLV08-94	BGKcLV08-94
ENCODE_alias	brenton-graveley:GNL3-BGKcLV08	brenton-graveley:GNL3-BGKcLV08-93	brenton-graveley:L-GNL3-BGKcLV08-93	brenton-graveley:GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGKcLV08-K562	brenton-graveley:GNL3-BGKcLV08-94	brenton-graveley:L-GNL3-BGKcLV08-94	brenton-graveley:GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR455VFL	ENCBS012JTK	ENCLB263GGR	ENCFF036FUU	ENCFF669NRA	ENCSR591RYB	ENCBS252OKO	ENCLB233CXM	ENCFF639RYW	ENCFF176UEM
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	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-93	BGKcLV08-94	BGKcLV08-94	BGKcLV08-94	BGKcLV08-94
Sample Name	GNL3-BGKcLV08-93	GNL3-BGKcLV08-93	GNL3-BGKcLV08-93	GNL3-BGKcLV08-93	GNL3-BGKcLV08-93	GNL3-BGKcLV08-93	GNL3-BGKcLV08-94	GNL3-BGKcLV08-94	GNL3-BGKcLV08-94	GNL3-BGKcLV08-94
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		GNL3-BGKcLV08-93.pdf	L-GNL3-BGKcLV08-93.pdf				GNL3-BGKcLV08-94.pdf	L-GNL3-BGKcLV08-94.pdf
ID	1128	1176	1246	1316	1386	7234	1177	1247	1317	1387

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	291				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	523
GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	291				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	593
GNL3-BGKcLV08-93_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26761
GNL3-BGKcLV08-93_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93/Aligned.sortedByCoord.out.bam		ENCORE2	26831
GNL3-BGKcLV08-93_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93/Aligned.sortedByCoord.out.bam		ENCORE2	26901
GNL3-BGKcLV08-93_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93/Aligned.sortedByCoord.out.bam		ENCORE2	26971
GNL3-BGKcLV08-93_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93/Aligned.sortedByCoord.out.bam		ENCORE2	27041
GNL3-BGKcLV08-93_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	291	GRCh38	V40	GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGKcLV08-93_AGCCTCAT+AGTAGAGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27111
GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	292				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	524
GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	292				NT-BGKcLV08-1_CCGCGGTT+AGCGCTAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV08-2_TTATAACC+GATATCGA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	594
GNL3-BGKcLV08-94_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26762
GNL3-BGKcLV08-94_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94/Aligned.sortedByCoord.out.bam		ENCORE2	26832
GNL3-BGKcLV08-94_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94/Aligned.sortedByCoord.out.bam		ENCORE2	26902
GNL3-BGKcLV08-94_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94/Aligned.sortedByCoord.out.bam		ENCORE2	26972
GNL3-BGKcLV08-94_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94/Aligned.sortedByCoord.out.bam		ENCORE2	27042
GNL3-BGKcLV08-94_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	292	GRCh38	V40	GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGKcLV08-94_GATTCTGC+GACGAGAG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27112