GEMIN5 RNA-Seq in K562

General Information


RBP	GEMIN5
Cell_Line	K562
Method	shRNA
Exp_Name	GEMIN5-BGKLV19-K562
ENCODE_series_ID	ENCSR817ZSP
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR398GHW
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	GEMIN5_BGKLV19_31B
Rep2	GEMIN5_BGKLV19_32B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	78.9
Rep2_qPCR	76.6
Rep1_WB	85.5
Rep2_WB	92.9
Antibody Cat#	A301-325A
Antibody Lot#	A301-325A
Antibody DCC ID	ENCAB395KQN
Status	Released
Project	ENCODE3
ID	474

Experiment Information (Status: Released)

	BGKLV19-31	BGKLV19-32
idx	238	239
TRCN#_or_BGC#	TRCN0000150146	TRCN0000150146
shRNA_or_gRNA_sequence	GCTGATGTTGAGGAAAGATTT	GCTGATGTTGAGGAAAGATTT
PAM
Name	GEMIN5	GEMIN5
Sample_ID	BGKLV19-31	BGKLV19-32
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	GEMIN5	GEMIN5
qPCR_result	78.9	76.6
Ave_qPCR	77.7
RT-qPCR_primer-F	atccactccatagcctggtg
RT-qPCR_primer-R	ttcccgttggtaatttcagc
protein_conc	2879	3177
WB_result	85.5	92.9
Ave_WB	89.2
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	18.0691161	0
Rep2_TPM	5.78614931	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	263	264

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-31	BGKLV19-32
Sample_ID	BGKLV19-31	BGKLV19-32
Sample Name	GEMIN5_BGKLV19_31B	GEMIN5_BGKLV19_32B
Sample Name	GEMIN5_BGKLV19_31B	GEMIN5_BGKLV19_32B
RBP	GEMIN5	GEMIN5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	678	679

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-31	BGKLV19-32
Sample #
Sample Name	GEMIN5-BGKLV19-31B	GEMIN5-BGKLV19-32B
Sample_Name_Alias	GEMIN5_BGKLV19_31B	GEMIN5_BGKLV19_32B
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/C9.png	DNA_Library_LV18-19/set1/D9.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G3.png	RNA_Library_LV19-21-24/set1/H3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-31	BGKLV19-32
RBP	GEMIN5	GEMIN5
Batch_ID	BGKLV19	BGKLV19
WB_result	85.500	92.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2364	2365

Sequencing Information

	BGKLV19-31	BGKLV19-32
Sample_ID	BGKLV19-31	BGKLV19-32
Sample Name	GEMIN5_BGKLV19_31B	GEMIN5_BGKLV19_32B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	49,650,000	45,930,000
total_aligned_reads	45,937,752	41,878,370
unique_aligned_reads	42,245,382	38,425,552
percent_uniqueAligned	0.85086	0.83661
correlation_replicates	0.999400	0.999400
spikein_reads	220,388	113,572
percent_spikeins	0.00444	0.00247
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1006	1007

Data Submission Information

	BGKLV19-31	BGKLV19-31
ENCODE_alias	brenton-graveley:GEMIN5_BGKLV19	brenton-graveley:GEMIN5-BGKLV19-K562
ENCODE_accession	ENCSR398GHW	ENCSR817ZSP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-31	BGKLV19-31
Sample Name	GEMIN5_BGKLV19_31B	GEMIN5_BGKLV19_31B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2888	6732

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_BGKLV19_31B_GTGGCC_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1006	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15118
GEMIN5_BGKLV19_31B_GTGGCC_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1006	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15176
GEMIN5_BGKLV19_31B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B_GTGGCC_L004_R1_001.fastq.gz,GEMIN5_BGKLV19_31B_GTGGCC_L004_R2_001.fastq.gz		ENCORE2	15234
GEMIN5_BGKLV19_31B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B/Aligned.sortedByCoord.out.bam		ENCORE2	15305
GEMIN5_BGKLV19_31B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B/Aligned.sortedByCoord.out.bam		ENCORE2	15363
GEMIN5_BGKLV19_31B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B/Aligned.sortedByCoord.out.bam		ENCORE2	15421
GEMIN5_BGKLV19_31B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B/Aligned.sortedByCoord.out.bam		ENCORE2	15479
GEMIN5_BGKLV19_31B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1006					GRCh38	V40	GEMIN5_BGKLV19_31B_GTGGCC_L004_R1_001.fastq.gz,GEMIN5_BGKLV19_31B_GTGGCC_L004_R2_001.fastq.gz		ENCORE2	16376
GEMIN5_BGKLV19_32B_GTTTCG_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1007	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15119
GEMIN5_BGKLV19_32B_GTTTCG_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1007	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15177
GEMIN5_BGKLV19_32B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B_GTTTCG_L004_R1_001.fastq.gz,GEMIN5_BGKLV19_32B_GTTTCG_L004_R2_001.fastq.gz		ENCORE2	15235
GEMIN5_BGKLV19_32B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B/Aligned.sortedByCoord.out.bam		ENCORE2	15306
GEMIN5_BGKLV19_32B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B/Aligned.sortedByCoord.out.bam		ENCORE2	15364
GEMIN5_BGKLV19_32B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B/Aligned.sortedByCoord.out.bam		ENCORE2	15422
GEMIN5_BGKLV19_32B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B/Aligned.sortedByCoord.out.bam		ENCORE2	15480
GEMIN5_BGKLV19_32B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1007					GRCh38	V40	GEMIN5_BGKLV19_32B_GTTTCG_L004_R1_001.fastq.gz,GEMIN5_BGKLV19_32B_GTTTCG_L004_R2_001.fastq.gz		ENCORE2	16377