EXOSC5 RNA-Seq in K562

General Information


RBP	EXOSC5
Cell_Line	K562
Method	CRISPR
Exp_Name	EXOSC5-BGKcLV06-K562
ENCODE_series_ID	ENCSR938MFO
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR406SEH
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	EXOSC5-BGKcLV06-13
Rep2	EXOSC5-BGKcLV06-14
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	77.7
Rep2_WB	81.4
Antibody Cat#	RN100PW
Antibody Lot#
Antibody DCC ID	ENCAB480FQK
Status	Released
Project	ENCODE3
ID	772

Experiment Information (Status: Released)

	BGKcLV06-13	BGKcLV06-14
idx	189	190
TRCN#_or_BGC#	BGC#0000093	BGC#0000093
shRNA_or_gRNA_sequence	AGCCATCTGGCCGCGACAGC	AGCCATCTGGCCGCGACAGC
PAM
Name	EXOSC5_91	EXOSC5_91
Sample_ID	BGKcLV06-13	BGKcLV06-14
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	EXOSC5	EXOSC5
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	cagatggctctgcttccttc
RT-qPCR_primer-R	acttcgagtgtggccttgtt
protein_conc	2881	3099
WB_result	77.7	81.4
Ave_WB	79.5
WB_DONE_date	6/27/17
MW	25kd
IP
antibody_Cat#	RN100PW
Antibody DCC ID	ENCAB480FQK	ENCAB480FQK
submitted_to_DCC_date	9/29/17
Rep1_TPM	34.4	0
Rep2_TPM	15	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4287	4288

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC5	Product_ID: RN100PW Lot_ID: 1 Source: MBLI Target Name: EXOSC5-human

Experiment Status

	BGKcLV06-13	BGKcLV06-14
Sample_ID	BGKcLV06-13	BGKcLV06-14
Sample Name	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-14
Sample Name	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-14
RBP	EXOSC5	EXOSC5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1359	1360

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-13	BGKcLV06-14
Sample #
Sample Name	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-14
Sample_Name_Alias	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-14
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/C1.png	DNA_Library_set39/set2/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set39/set3/D1.png	RNA_Library_set39/set3/E1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-13	BGKcLV06-14
RBP	EXOSC5	EXOSC5
Batch_ID	BGKcLV06	BGKcLV06
WB_result	77.700	81.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3054	3055

Sequencing Information

	BGKcLV06-13	BGKcLV06-14
Sample_ID	BGKcLV06-13	BGKcLV06-14
Sample Name	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-14
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	60,901,668	53,967,358
total_aligned_reads	52,641,370	47,541,116
unique_aligned_reads	47,945,680	43,472,090
percent_uniqueAligned	0.78726	0.80553
correlation_replicates	0.996039	0.996039
spikein_reads	29,080	21,652
percent_spikeins	0.00048	0.00040
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1705	1706

Data Submission Information

	BGKcLV06-13	BGKcLV06-13
ENCODE_alias	brenton-graveley:EXOSC5-BGKcLV06	brenton-graveley:EXOSC5-BGKcLV06-K562
ENCODE_accession	ENCSR406SEH	ENCSR938MFO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-13	BGKcLV06-13
Sample Name	EXOSC5-BGKcLV06-13	EXOSC5-BGKcLV06-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3219	6703

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
EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1705	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22464
EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1705	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22500
EXOSC5-BGKcLV06-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R1.fastq.gz,EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22536
EXOSC5-BGKcLV06-13_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	22572
EXOSC5-BGKcLV06-13_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	22608
EXOSC5-BGKcLV06-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	22644
EXOSC5-BGKcLV06-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13/Aligned.sortedByCoord.out.bam		ENCORE2	22680
EXOSC5-BGKcLV06-13_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1705					GRCh38	V40	EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R1.fastq.gz,EXOSC5-BGKcLV06-13_GGCTAC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22716
EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1706	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22465
EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1706	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22501
EXOSC5-BGKcLV06-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R1.fastq.gz,EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22537
EXOSC5-BGKcLV06-14_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	22573
EXOSC5-BGKcLV06-14_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	22609
EXOSC5-BGKcLV06-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	22645
EXOSC5-BGKcLV06-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14/Aligned.sortedByCoord.out.bam		ENCORE2	22681
EXOSC5-BGKcLV06-14_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1706					GRCh38	V40	EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R1.fastq.gz,EXOSC5-BGKcLV06-14_CTTGTA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22717