GNL3 RNA-Seq in HepG2

General Information


RBP	GNL3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GNL3-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR008UZG
Batch_ID	BGHcLV05
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR940FIN
ENCODE_CN_Exp_ID	ENCSR713OTF
Rep1	GNL3-BGHcLV05-19E
Rep2	GNL3-BGHcLV05-20E
CN1	NT-BGHcLV05-1E
CN2	NT-BGHcLV05-2E
Rep1_qPCR	66.7
Rep2_qPCR	66.8
Rep1_WB	100.0
Rep2_WB	100.0
Antibody Cat#	A300-599A
Antibody Lot#	A300-599A
Antibody DCC ID	ENCAB664GBP
Status	Released
Project	ENCODE4
ID	98

Experiment Information (Status: Released)

	BGHcLV05-19	BGHcLV05-19	BGHcLV05-20	BGHcLV05-20
idx	55	94	56	95
TRCN#_or_BGC#	BGC#0000038	BGC#0000038	BGC#0000038	BGC#0000038
shRNA_or_gRNA_sequence	CACCTCTAGGACAACATCGG	CACCTCTAGGACAACATCGG	CACCTCTAGGACAACATCGG	CACCTCTAGGACAACATCGG
PAM
Name	GNL3_6	GNL3_6	GNL3_6	GNL3_6
Sample_ID	BGHcLV05-19	BGHcLV05-19	BGHcLV05-20	BGHcLV05-20
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	GNL3	GNL3	GNL3	GNL3
qPCR_result	66.7		66.8
Ave_qPCR	66.7
RT-qPCR_primer-F	cccaggagttccaaacagtg
RT-qPCR_primer-R	tgcctgtcaagtttctgctg
protein_conc	4236	0	4189	0
WB_result	100.0		100.0
Ave_WB	100.0
WB_DONE_date	7/20/16		WES
MW	62 kDa
IP	1
antibody_Cat#	A300-599A		A300-599A
Antibody DCC ID	ENCAB664GBP		ENCAB664GBP
submitted_to_DCC_date	10/26/16
Rep1_TPM	196	0	0	0
Rep2_TPM	168	0	0	0
Action	Ready		Ready
Library_start_date	08/15/16		08/15/16
repeat_library	12/5/19		12/5/19
Note
ID	6198	6235	6199	6236

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

	BGHcLV05-19	BGHcLV05-20
Sample_ID	BGHcLV05-19	BGHcLV05-20
Sample Name
Sample Name	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-20E
RBP	GNL3	GNL3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5678	5679

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-19	BGHcLV05-20
Sample #	39	40
Sample Name	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-20E
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-A1	1-B1
Tecan	29.00	24.57
Tecan_date	2019-12-16	2019-12-16
Size_bp	282	286
Peak_Molarity	29.80	29.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E11.png	DNA_Library_set43-44/set1/F11.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_set43-44/set5/A1.png	RNA_Library_set43-44/set5/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGHcLV05-19	BGHcLV05-20
RBP	GNL3	GNL3
Batch_ID	BGHcLV05	BGHcLV05
WB_result	100.000	100.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	E	E
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	615	616

Sequencing Information

	BGHcLV05-19	BGHcLV05-20
Sample_ID	BGHcLV05-19	BGHcLV05-20
Sample Name	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-20E
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	126,862,978	307,412,356
total_aligned_reads	123,870,222	297,046,164
unique_aligned_reads	116,329,204	279,379,496
percent_uniqueAligned	0.91697	0.90881
correlation_replicates	0.996469	0.996469
spikein_reads	40,708	69,698
percent_spikeins	0.00032	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	167	168

Data Submission Information

	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-20	BGHcLV05-20	BGHcLV05-20	BGHcLV05-20
ENCODE_alias	brenton-graveley:GNL3-BGHcLV05-E	brenton-graveley:GNL3-BGHcLV05-19E	brenton-graveley:L-GNL3-BGHcLV05-19E	brenton-graveley:GNL3-BGHcLV05-19E_S31_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGHcLV05-19E_S31_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGHcLV05-HepG2	brenton-graveley:GNL3-BGHcLV05-20E	brenton-graveley:L-GNL3-BGHcLV05-20E	brenton-graveley:GNL3-BGHcLV05-20E_S32_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GNL3-BGHcLV05-20E_S32_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR940FIN	ENCBS399GKJ	ENCLB879TDQ	ENCFF478WDZ	ENCFF499XEL	ENCSR008UZG	ENCBS564UDY	ENCLB020NCM	ENCFF415JDH	ENCFF967JUQ
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	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-19	BGHcLV05-20	BGHcLV05-20	BGHcLV05-20	BGHcLV05-20
Sample Name	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-19E	GNL3-BGHcLV05-20E	GNL3-BGHcLV05-20E	GNL3-BGHcLV05-20E	GNL3-BGHcLV05-20E
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		GNL3-BGHcLV05-19E.pdf	L-GNL3-BGHcLV05-19E.pdf				GNL3-BGHcLV05-20E.pdf	L-GNL3-BGHcLV05-20E.pdf
ID	44	168	332	584	636	7233	169	333	585	637

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
GNL3-BGHcLV05-19E_S31_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	167	NovaSeq6000	100	paired-ended	1				NT-BGHcLV05-1E_S33_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2E_S34_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	191
GNL3-BGHcLV05-19E_S31_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	167	NovaSeq6000	100	paired-ended	2				NT-BGHcLV05-1E_S33_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2E_S34_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	243
GNL3-BGHcLV05-19E_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E_S31_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGHcLV05-19E_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24911
GNL3-BGHcLV05-19E_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E/Aligned.sortedByCoord.out.bam		ENCORE2	24963
GNL3-BGHcLV05-19E_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E/Aligned.sortedByCoord.out.bam		ENCORE2	25015
GNL3-BGHcLV05-19E_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E/Aligned.sortedByCoord.out.bam		ENCORE2	25067
GNL3-BGHcLV05-19E_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E/Aligned.sortedByCoord.out.bam		ENCORE2	25119
GNL3-BGHcLV05-19E_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	167					GRCh38	V40	GNL3-BGHcLV05-19E_S31_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGHcLV05-19E_S31_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25171
GNL3-BGHcLV05-20E_S32_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	168	NovaSeq6000	100	paired-ended	1				NT-BGHcLV05-1E_S33_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2E_S34_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	192
GNL3-BGHcLV05-20E_S32_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	168	NovaSeq6000	100	paired-ended	2				NT-BGHcLV05-1E_S33_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV05-2E_S34_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	244
GNL3-BGHcLV05-20E_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E_S32_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGHcLV05-20E_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24912
GNL3-BGHcLV05-20E_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E/Aligned.sortedByCoord.out.bam		ENCORE2	24964
GNL3-BGHcLV05-20E_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E/Aligned.sortedByCoord.out.bam		ENCORE2	25016
GNL3-BGHcLV05-20E_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E/Aligned.sortedByCoord.out.bam		ENCORE2	25068
GNL3-BGHcLV05-20E_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E/Aligned.sortedByCoord.out.bam		ENCORE2	25120
GNL3-BGHcLV05-20E_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	168					GRCh38	V40	GNL3-BGHcLV05-20E_S32_R1_001.filtered.trimmed.paired.fastq.gz,GNL3-BGHcLV05-20E_S32_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25172