GEMIN2 RNA-Seq in HepG2

General Information


RBP	GEMIN2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	GEMIN2-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR810ZMS
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR333OGA
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	GEMIN2-BGHcLV18-25
Rep2	GEMIN2-BGHcLV18-26
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	21.0
Rep2_qPCR	0.0
Rep1_WB	87.9
Rep2_WB	89.5
Antibody Cat#	RN102PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB284NOX
Status	Released
Project	ENCODE4
ID	109

Experiment Information (Status: Released)

	BGHcLV18-25	BGHcLV18-26
idx	518	519
TRCN#_or_BGC#	BGC#0000419	BGC#0000419
shRNA_or_gRNA_sequence	TCGATCCCTCGGTACCCCCG	TCGATCCCTCGGTACCCCCG
PAM	AGG	AGG
Name	GEMIN2_95	GEMIN2_95
Sample_ID	BGHcLV18-25	BGHcLV18-26
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	GEMIN2	GEMIN2
qPCR_result	21.0	0.0
Ave_qPCR	10.5
RT-qPCR_primer-F	CTGTTGGACCAGCCACAAA
RT-qPCR_primer-R	CTAAGCAAGGGAGGAAAACCA
protein_conc	3854	3852
WB_result	87.9	89.5
Ave_WB	88.7
WB_DONE_date	10/2/20
MW	32KD
IP	Rabbit / I
antibody_Cat#	RN102PW	lot #1
Antibody DCC ID	ENCAB284NOX
submitted_to_DCC_date
Rep1_TPM	50	0
Rep2_TPM	80	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6671	6672

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

	BGHcLV18-25	BGHcLV18-26
Sample_ID	BGHcLV18-25	BGHcLV18-26
Sample Name	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-26
Sample Name	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-26
RBP	GEMIN2	GEMIN2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5635	5636

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-25	BGHcLV18-26
Sample #	141	142
Sample Name	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-26
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-A2	4-B2
Tecan	37.61	33.76
Tecan_date	2019-12-16	2019-12-16
Size_bp	271	281
Peak_Molarity	32.90	28.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E10.png	DNA_Library_set43-44/set2/F10.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/A12.png	RNA_Library_set43-44/set4/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-25	BGHcLV18-26
RBP	GEMIN2	GEMIN2
Batch_ID	BGHcLV18	BGHcLV18
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	717	718

Sequencing Information

	BGHcLV18-25	BGHcLV18-26
Sample_ID	BGHcLV18-25	BGHcLV18-26
Sample Name	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-26
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	158,262,902	156,318,140
total_aligned_reads	154,267,046	148,776,588
unique_aligned_reads	144,692,212	139,482,548
percent_uniqueAligned	0.91425	0.89230
correlation_replicates	0.996400	0.996400
spikein_reads	281,624	241,846
percent_spikeins	0.00178	0.00155
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	223	224

Data Submission Information

	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-26	BGHcLV18-26	BGHcLV18-26	BGHcLV18-26
ENCODE_alias	brenton-graveley:GEMIN2-BGHcLV18	brenton-graveley:GEMIN2-BGHcLV18-25	brenton-graveley:L-GEMIN2-BGHcLV18-25	brenton-graveley:GEMIN2-BGHcLV18-25_S79_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGHcLV18-25_S79_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGHcLV18-HepG2	brenton-graveley:GEMIN2-BGHcLV18-26	brenton-graveley:L-GEMIN2-BGHcLV18-26	brenton-graveley:GEMIN2-BGHcLV18-26_S80_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:GEMIN2-BGHcLV18-26_S80_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR333OGA	ENCBS940CPB	ENCLB615FAR	ENCFF383ZUF	ENCFF090KME	ENCSR810ZMS	ENCBS574RYJ	ENCLB512NMH	ENCFF312WCL	ENCFF592KCD
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	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-25	BGHcLV18-26	BGHcLV18-26	BGHcLV18-26	BGHcLV18-26
Sample Name	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-25	GEMIN2-BGHcLV18-26	GEMIN2-BGHcLV18-26	GEMIN2-BGHcLV18-26	GEMIN2-BGHcLV18-26
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		GEMIN2-BGHcLV18-25.pdf	L-GEMIN2-BGHcLV18-25.pdf				GEMIN2-BGHcLV18-26.pdf	L-GEMIN2-BGHcLV18-26.pdf
ID	56	192	358	608	660	7230	193	359	609	661

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-BGHcLV18-25_S79_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	223	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	189
GEMIN2-BGHcLV18-25_S79_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	223	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	241
GEMIN2-BGHcLV18-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	223					GRCh38	V40	GEMIN2-BGHcLV18-25_S79_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGHcLV18-25_S79_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24909
GEMIN2-BGHcLV18-25_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	223					GRCh38	V40	GEMIN2-BGHcLV18-25/Aligned.sortedByCoord.out.bam		ENCORE2	24961
GEMIN2-BGHcLV18-25_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	223					GRCh38	V40	GEMIN2-BGHcLV18-25/Aligned.sortedByCoord.out.bam		ENCORE2	25013
GEMIN2-BGHcLV18-25_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	223					GRCh38	V40	GEMIN2-BGHcLV18-25/Aligned.sortedByCoord.out.bam		ENCORE2	25065
GEMIN2-BGHcLV18-25_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	223					GRCh38	V40	GEMIN2-BGHcLV18-25/Aligned.sortedByCoord.out.bam		ENCORE2	25117
GEMIN2-BGHcLV18-25_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	223					GRCh38	V40	GEMIN2-BGHcLV18-25_S79_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGHcLV18-25_S79_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25169
GEMIN2-BGHcLV18-26_S80_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	224	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	190
GEMIN2-BGHcLV18-26_S80_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	224	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	242
GEMIN2-BGHcLV18-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	224					GRCh38	V40	GEMIN2-BGHcLV18-26_S80_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGHcLV18-26_S80_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24910
GEMIN2-BGHcLV18-26_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	224					GRCh38	V40	GEMIN2-BGHcLV18-26/Aligned.sortedByCoord.out.bam		ENCORE2	24962
GEMIN2-BGHcLV18-26_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	224					GRCh38	V40	GEMIN2-BGHcLV18-26/Aligned.sortedByCoord.out.bam		ENCORE2	25014
GEMIN2-BGHcLV18-26_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	224					GRCh38	V40	GEMIN2-BGHcLV18-26/Aligned.sortedByCoord.out.bam		ENCORE2	25066
GEMIN2-BGHcLV18-26_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	224					GRCh38	V40	GEMIN2-BGHcLV18-26/Aligned.sortedByCoord.out.bam		ENCORE2	25118
GEMIN2-BGHcLV18-26_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	224					GRCh38	V40	GEMIN2-BGHcLV18-26_S80_R1_001.filtered.trimmed.paired.fastq.gz,GEMIN2-BGHcLV18-26_S80_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25170