GEMIN5 RNA-Seq in HepG2

General Information


RBP	GEMIN5
Cell_Line	HepG2
Method	shRNA
Exp_Name	GEMIN5-BGHLV16-HepG2
ENCODE_series_ID	ENCSR560CDR
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR771QMJ
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	GEMIN5_BGHLV16_29
Rep2	GEMIN5_BGHLV16_30
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	56.5
Rep2_qPCR	55.9
Rep1_WB	89.2
Rep2_WB	83.3
Antibody Cat#	A301-325A
Antibody Lot#	A301-325A
Antibody DCC ID	ENCAB395KQN
Status	Released
Project	ENCODE3
ID	419

Experiment Information (Status: Released)

	BGHLV16-29	BGHLV16-30
idx	197	198
TRCN#_or_BGC#	TRCN0000150146	TRCN0000150146
shRNA_or_gRNA_sequence	GCTGATGTTGAGGAAAGATTT	GCTGATGTTGAGGAAAGATTT
PAM
Name	GEMIN5	GEMIN5
Sample_ID	BGHLV16-29	BGHLV16-30
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	GEMIN5	GEMIN5
qPCR_result	56.5	55.9
Ave_qPCR	56.2
RT-qPCR_primer-F	atccactccatagcctggtg
RT-qPCR_primer-R	ttcccgttggtaatttcagc
protein_conc	2733	3196
WB_result	89.2	83.3
Ave_WB	86.3
WB_DONE_date	1/7/2015
MW	169kDa
IP	1	1
antibody_Cat#	A301-325A	A301-325A
Antibody DCC ID	ENCAB395KQN	ENCAB395KQN
submitted_to_DCC_date	4/2/2015
Rep1_TPM	6.2	0
Rep2_TPM	6.3	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2262	2263

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GEMIN5	Product_ID: A301-325A Lot_ID: 1 Source: Bethyl Labs Target Name: GEMIN5-human

Experiment Status

	BGHLV16-29	BGHLV16-30
Sample_ID	BGHLV16-29	BGHLV16-30
Sample Name	GEMIN5_BGHLV16_29	GEMIN5_BGHLV16_30
Sample Name	GEMIN5_BGHLV16_29	GEMIN5_BGHLV16_30
RBP	GEMIN5	GEMIN5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	562	563

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-29	BGHLV16-30
Sample #
Sample Name	GEMIN5-BGHLV16-29	GEMIN5-BGHLV16-30
Sample_Name_Alias	GEMIN5_BGHLV16_29	GEMIN5_BGHLV16_30
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/E7.png	DNA_Library_LV16-17/set1/F7.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C1.png	RNA_Library_LV16-17-18/set1/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-29	BGHLV16-30
RBP	GEMIN5	GEMIN5
Batch_ID	BGHLV16	BGHLV16
WB_result	89.200	83.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2246	2247

Sequencing Information

	BGHLV16-29	BGHLV16-30
Sample_ID	BGHLV16-29	BGHLV16-30
Sample Name	GEMIN5_BGHLV16_29	GEMIN5_BGHLV16_30
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set16	set16
total_reads	54,380,000	32,020,000
total_aligned_reads	43,695,032	25,304,506
unique_aligned_reads	41,049,470	23,777,330
percent_uniqueAligned	0.75486	0.74258
correlation_replicates	0.998643	0.998643
spikein_reads	73,578	58,438
percent_spikeins	0.00135	0.00183
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	888	889

Data Submission Information

	BGHLV16-29	BGHLV16-29
ENCODE_alias	brenton-graveley:GEMIN5_BGHLV16	brenton-graveley:GEMIN5-BGHLV16-HepG2
ENCODE_accession	ENCSR771QMJ	ENCSR560CDR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-29	BGHLV16-29
Sample Name	GEMIN5_BGHLV16_29	GEMIN5_BGHLV16_29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2849	6731

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
GEMIN5_BGHLV16_29_AGTCAA_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	888	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14288
GEMIN5_BGHLV16_29_AGTCAA_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	888	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14314
GEMIN5_BGHLV16_29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29_AGTCAA_L007_R1_001.fastq.gz,GEMIN5_BGHLV16_29_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	14340
GEMIN5_BGHLV16_29_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29/Aligned.sortedByCoord.out.bam		ENCORE2	14366
GEMIN5_BGHLV16_29_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29/Aligned.sortedByCoord.out.bam		ENCORE2	14392
GEMIN5_BGHLV16_29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29/Aligned.sortedByCoord.out.bam		ENCORE2	14418
GEMIN5_BGHLV16_29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29/Aligned.sortedByCoord.out.bam		ENCORE2	14444
GEMIN5_BGHLV16_29_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	888					GRCh38	V40	GEMIN5_BGHLV16_29_AGTCAA_L007_R1_001.fastq.gz,GEMIN5_BGHLV16_29_AGTCAA_L007_R2_001.fastq.gz		ENCORE2	14470
GEMIN5_BGHLV16_30_AGTTCC_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	889	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14289
GEMIN5_BGHLV16_30_AGTTCC_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	889	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14315
GEMIN5_BGHLV16_30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30_AGTTCC_L007_R1_001.fastq.gz,GEMIN5_BGHLV16_30_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	14341
GEMIN5_BGHLV16_30_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30/Aligned.sortedByCoord.out.bam		ENCORE2	14367
GEMIN5_BGHLV16_30_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30/Aligned.sortedByCoord.out.bam		ENCORE2	14393
GEMIN5_BGHLV16_30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30/Aligned.sortedByCoord.out.bam		ENCORE2	14419
GEMIN5_BGHLV16_30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30/Aligned.sortedByCoord.out.bam		ENCORE2	14445
GEMIN5_BGHLV16_30_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	889					GRCh38	V40	GEMIN5_BGHLV16_30_AGTTCC_L007_R1_001.fastq.gz,GEMIN5_BGHLV16_30_AGTTCC_L007_R2_001.fastq.gz		ENCORE2	14471