EXOSC5 RNA-Seq in HepG2

General Information


RBP	EXOSC5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EXOSC5-BGHcLV07-HepG2
ENCODE_series_ID	ENCSR172JHG
Batch_ID	BGHcLV07
Pool ID	Pool-170911
Local_Set_Name	set39_H
ENCODE_KD_Exp_ID	ENCSR284SZO
ENCODE_CN_Exp_ID	ENCSR521WAI
Rep1	EXOSC5-BGHcLV07-13
Rep2	EXOSC5-BGHcLV07-14
CN1	NT-BGHcLV07-1
CN2	NT-BGHcLV07-2
Rep1_qPCR	32.5
Rep2_qPCR	47.9
Rep1_WB	56.9
Rep2_WB	60.5
Antibody Cat#	RN100PW
Antibody Lot#
Antibody DCC ID	ENCAB480FQK
Status	Released
Project	ENCODE3
ID	764

Experiment Information (Status: Released)

	BGHcLV07-13	BGHcLV07-14
idx	125	126
TRCN#_or_BGC#	BGC#0000094	BGC#0000094
shRNA_or_gRNA_sequence	GTTCGCAGGCAAAGTGCCGG	GTTCGCAGGCAAAGTGCCGG
PAM
Name	EXOSC5_90-1	EXOSC5_90-1
Sample_ID	BGHcLV07-13	BGHcLV07-14
transduction_Date	6/13/17	6/13/17
days	D6	D6
RBP_name	EXOSC5	EXOSC5
qPCR_result	32.5	47.9
Ave_qPCR	40.2
RT-qPCR_primer-F	cagatggctctgcttccttc
RT-qPCR_primer-R	acttcgagtgtggccttgtt
protein_conc	3613	3762
WB_result	56.9	60.5
Ave_WB	58.7
WB_DONE_date	6/27/17
MW	25kd
IP
antibody_Cat#	RN100PW
Antibody DCC ID	ENCAB480FQK
submitted_to_DCC_date	9/27/17
Rep1_TPM	20	0
Rep2_TPM	5	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	6266	6267

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

	BGHcLV07-13	BGHcLV07-14
Sample_ID	BGHcLV07-13	BGHcLV07-14
Sample Name	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-14
Sample Name	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-14
RBP	EXOSC5	EXOSC5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1381	1382

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV07-13	BGHcLV07-14
Sample #
Sample Name	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-14
Sample_Name_Alias	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-14
Index Well Position	S09	S10
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/A4.png	DNA_Library_set39/set2/B4.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set39/set2/C1.png	RNA_Library_set39/set2/D1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHcLV07-13	BGHcLV07-14
RBP	EXOSC5	EXOSC5
Batch_ID	BGHcLV07	BGHcLV07
WB_result	56.900	60.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3076	3077

Sequencing Information

	BGHcLV07-13	BGHcLV07-14
Sample_ID	BGHcLV07-13	BGHcLV07-14
Sample Name	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-14
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_H	set39_H
total_reads	60,197,284	47,672,616
total_aligned_reads	51,278,944	40,652,524
unique_aligned_reads	48,373,086	38,348,528
percent_uniqueAligned	0.80358	0.80441
correlation_replicates	0.982013	0.982013
spikein_reads	21,666	12,484
percent_spikeins	0.00036	0.00026
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1727	1728

Data Submission Information

	BGHcLV07-13	BGHcLV07-13
ENCODE_alias	brenton-graveley:EXOSC5-BGHcLV07	brenton-graveley:EXOSC5-BGHcLV07-HepG2
ENCODE_accession	ENCSR284SZO	ENCSR172JHG
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV07-13	BGHcLV07-13
Sample Name	EXOSC5-BGHcLV07-13	EXOSC5-BGHcLV07-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3230	6702

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-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1727	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22274
EXOSC5-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1727	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22298
EXOSC5-BGHcLV07-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R1.fastq.gz,EXOSC5-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22322
EXOSC5-BGHcLV07-13_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	22346
EXOSC5-BGHcLV07-13_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	22370
EXOSC5-BGHcLV07-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	22394
EXOSC5-BGHcLV07-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13/Aligned.sortedByCoord.out.bam		ENCORE2	22418
EXOSC5-BGHcLV07-13_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1727					GRCh38	V40	EXOSC5-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R1.fastq.gz,EXOSC5-BGHcLV07-13_GATCAG_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22442
EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1728	HiSeq2500	100	paired-ended	1				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R1.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE3	22275
EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1728	HiSeq2500	100	paired-ended	2				NT-BGHcLV07-1_CAGATC_ACBE67ANXX_L007_001.R2.fastq.gz,NT-BGHcLV07-2_ACTTGA_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE3	22299
EXOSC5-BGHcLV07-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R1.fastq.gz,EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22323
EXOSC5-BGHcLV07-14_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	22347
EXOSC5-BGHcLV07-14_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	22371
EXOSC5-BGHcLV07-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	22395
EXOSC5-BGHcLV07-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14/Aligned.sortedByCoord.out.bam		ENCORE2	22419
EXOSC5-BGHcLV07-14_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1728					GRCh38	V40	EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R1.fastq.gz,EXOSC5-BGHcLV07-14_TAGCTT_ACBE67ANXX_L008_001.R2.fastq.gz		ENCORE2	22443