GEMIN2 RNA-Seq in K562

General Information


RBP	GEMIN2
Cell_Line	K562
Method	CRISPR
Exp_Name	GEMIN2-BGKcLV17-K562
ENCODE_series_ID	ENCSR576LAK
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR039SOI
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	GEMIN2-BGKcLV17-25
Rep2	GEMIN2-BGKcLV17-26
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	52.4
Rep2_qPCR	51.7
Rep1_WB	89.9
Rep2_WB	90.2
Antibody Cat#	RN102PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB284NOX
Status	Released
Project	ENCODE4
ID	87

Experiment Information (Status: Released)

	BGKcLV17-25	BGKcLV17-26
idx	632	633
TRCN#_or_BGC#	BGC#0000419	BGC#0000419
shRNA_or_gRNA_sequence	TCGATCCCTCGGTACCCCCG	TCGATCCCTCGGTACCCCCG
PAM	AGG	AGG
Name	GEMIN2_95	GEMIN2_95
Sample_ID	BGKcLV17-25	BGKcLV17-26
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	GEMIN2	GEMIN2
qPCR_result	52.4	51.7
Ave_qPCR	52.1
RT-qPCR_primer-F	CTGTTGGACCAGCCACAAA
RT-qPCR_primer-R	CTAAGCAAGGGAGGAAAACCA
protein_conc	3464	3727
WB_result	89.9	90.2
Ave_WB	90.1
WB_DONE_date	7/9/10
MW	32KD
IP	Rabbit / I
antibody_Cat#	RN102PW	lot #1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	27.3	0
Rep2_TPM	30.8	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4748	4749

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GEMIN2	Product_ID: RN102PW Lot_ID: 1 Source: MBLI Target Name: GEMIN2-human

Experiment Status

	BGKcLV17-25	BGKcLV17-26
Sample_ID	BGKcLV17-25	BGKcLV17-26
Sample Name
Sample Name	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-26
RBP	GEMIN2	GEMIN2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5507	5508

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-25	BGKcLV17-26
Sample #	97	98
Sample Name	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-26
Sample_Name_Alias
Index Well Position	G12	H12
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-E2	1-F2
Tecan	32.93	18.26
Tecan_date	2019-12-16	2019-12-16
Size_bp	275	281
Peak_Molarity	34.10	19.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G8.png	DNA_Library_set43-44/set1/H8.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/G3.png	RNA_Library_set43-44/set4/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-25	BGKcLV17-26
RBP	GEMIN2	GEMIN2
Batch_ID	BGKcLV17	BGKcLV17
WB_result	89.900	90.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	673	674

Sequencing Information

	BGKcLV17-25	BGKcLV17-26
Sample_ID	BGKcLV17-25	BGKcLV17-26
Sample Name	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-26
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	108,112,726	254,049,938
total_aligned_reads	101,952,708	214,590,610
unique_aligned_reads	92,522,176	194,734,964
percent_uniqueAligned	0.85579	0.76652
correlation_replicates	0.994523	0.994523
spikein_reads	21,972	80,236
percent_spikeins	0.00020	0.00032
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	179	180

Data Submission Information

	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-26	BGKcLV17-26	BGKcLV17-26	BGKcLV17-26
ENCODE_alias	brenton-graveley:GEMIN2-BGKcLV17	brenton-graveley:GEMIN2-BGKcLV17-25	brenton-graveley:L-GEMIN2-BGKcLV17-25	brenton-graveley:GEMIN2-BGKcLV17-25_S9_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGKcLV17-25_S9_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGKcLV17-K562	brenton-graveley:GEMIN2-BGKcLV17-26	brenton-graveley:L-GEMIN2-BGKcLV17-26	brenton-graveley:GEMIN2-BGKcLV17-26_S10_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGKcLV17-26_S10_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR039SOI	ENCBS351JNN	ENCLB430SYI	ENCFF987NAI	ENCFF972DCE	ENCSR576LAK	ENCBS821IPB	ENCLB958LHT	ENCFF700SAR	ENCFF182KVY
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	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-25	BGKcLV17-26	BGKcLV17-26	BGKcLV17-26	BGKcLV17-26
Sample Name	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-25	GEMIN2-BGKcLV17-26	GEMIN2-BGKcLV17-26	GEMIN2-BGKcLV17-26	GEMIN2-BGKcLV17-26
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
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		GEMIN2-BGKcLV17-25.pdf	L-GEMIN2-BGKcLV17-25.pdf				GEMIN2-BGKcLV17-26.pdf	L-GEMIN2-BGKcLV17-26.pdf
ID	73	226	392	694	724	7231	227	393	695	725

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
GEMIN2-BGKcLV17-25_S9_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	179	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	281
GEMIN2-BGKcLV17-25_S9_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	179	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	311
GEMIN2-BGKcLV17-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25_S9_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGKcLV17-25_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24677
GEMIN2-BGKcLV17-25_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25/Aligned.sortedByCoord.out.bam		ENCORE2	24707
GEMIN2-BGKcLV17-25_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25/Aligned.sortedByCoord.out.bam		ENCORE2	24737
GEMIN2-BGKcLV17-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25/Aligned.sortedByCoord.out.bam		ENCORE2	24767
GEMIN2-BGKcLV17-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25/Aligned.sortedByCoord.out.bam		ENCORE2	24797
GEMIN2-BGKcLV17-25_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	179					GRCh38	V40	GEMIN2-BGKcLV17-25_S9_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGKcLV17-25_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24827
GEMIN2-BGKcLV17-26_S10_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	180	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	282
GEMIN2-BGKcLV17-26_S10_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	180	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	312
GEMIN2-BGKcLV17-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26_S10_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGKcLV17-26_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24678
GEMIN2-BGKcLV17-26_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26/Aligned.sortedByCoord.out.bam		ENCORE2	24708
GEMIN2-BGKcLV17-26_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26/Aligned.sortedByCoord.out.bam		ENCORE2	24738
GEMIN2-BGKcLV17-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26/Aligned.sortedByCoord.out.bam		ENCORE2	24768
GEMIN2-BGKcLV17-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26/Aligned.sortedByCoord.out.bam		ENCORE2	24798
GEMIN2-BGKcLV17-26_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	180					GRCh38	V40	GEMIN2-BGKcLV17-26_S10_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGKcLV17-26_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24828