EXOSC10 RNA-Seq in K562

General Information


RBP	EXOSC10
Cell_Line	K562
Method	CRISPR
Exp_Name	EXOSC10-BGKcLV21-K562
ENCODE_series_ID	ENCSR692SPC
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR299PRA
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	EXOSC10-BGKcLV21-21
Rep2	EXOSC10-BGKcLV21-22
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	60.5
Rep2_WB	65.1389045
Antibody Cat#	A303-987A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB270KRD
Status	Released
Project	ENCODE4
ID	67

Experiment Information (Status: Released)

	BGKcLV21-21	BGKcLV21-22
idx	754	755
TRCN#_or_BGC#	BGC#0000516	BGC#0000516
shRNA_or_gRNA_sequence	TAATGTTGCTGCGACACCCA	TAATGTTGCTGCGACACCCA
PAM	TGG	TGG
Name	EXOSC10_93	EXOSC10_93
Sample_ID	BGKcLV21-21	BGKcLV21-22
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	EXOSC10	EXOSC10
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4586	4445
WB_result	60.5	65.1389045
Ave_WB	62.8
WB_DONE_date	10/9/20	JESS
MW	101kDa
IP	Rabbit / I
antibody_Cat#	A303-987A	Lot# 1
Antibody DCC ID	ENCAB270KRD
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4874	4875

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC10	Product_ID: A303-987A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC10-human

Experiment Status

	BGKcLV21-21	BGKcLV21-22
Sample_ID	BGKcLV21-21	BGKcLV21-22
Sample Name
Sample Name	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-22
RBP	EXOSC10	EXOSC10
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6125	6126

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-21	BGKcLV21-22
Sample #	43	44
Sample Name	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-22
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	299	309
Peak_Molarity	213.00	162.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E5.png	DNA_Library_set45/set2/H9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set45/set1/E5.png	RNA_Library_set45/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-21	BGKcLV21-22
RBP	EXOSC10	EXOSC10
Batch_ID	BGKcLV21	BGKcLV21
WB_result	73.800	65.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	817	818

Sequencing Information

	BGKcLV21-21	BGKcLV21-22
Sample_ID	BGKcLV21-21	BGKcLV21-22
Sample Name	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-22
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	142,926,356	123,753,022
total_aligned_reads	135,675,556	114,580,050
unique_aligned_reads	124,240,092	105,039,842
percent_uniqueAligned	0.86926	0.84879
correlation_replicates	0.982040	0.982040
spikein_reads	77,230	53,672
percent_spikeins	0.00054	0.00043
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	448	449

Data Submission Information

	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-22	BGKcLV21-22	BGKcLV21-22	BGKcLV21-22
ENCODE_alias	brenton-graveley:EXOSC10-BGKcLV21	brenton-graveley:EXOSC10-BGKcLV21-21	brenton-graveley:L-EXOSC10-BGKcLV21-21	brenton-graveley:EXOSC10-BGKcLV21-21_S37_R1_001.fastq.gz	brenton-graveley:EXOSC10-BGKcLV21-21_S37_R2_001.fastq.gz	brenton-graveley:EXOSC10-BGKcLV21-K562	brenton-graveley:EXOSC10-BGKcLV21-22	brenton-graveley:L-EXOSC10-BGKcLV21-22	brenton-graveley:EXOSC10-BGKcLV21-22_S38_R1_001.fastq.gz	brenton-graveley:EXOSC10-BGKcLV21-22_S38_R2_001.fastq.gz
ENCODE_accession	ENCSR299PRA	ENCBS311NMT	ENCLB218JPE	ENCFF467MIH	ENCFF503AZV	ENCSR692SPC	ENCBS470VBM	ENCLB410XQE	ENCFF380UNU	ENCFF860WTK
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	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-21	BGKcLV21-22	BGKcLV21-22	BGKcLV21-22	BGKcLV21-22
Sample Name	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-21	EXOSC10-BGKcLV21-22	EXOSC10-BGKcLV21-22	EXOSC10-BGKcLV21-22	EXOSC10-BGKcLV21-22
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		EXOSC10-BGKcLV21-21.pdf	L-EXOSC10-BGKcLV21-21.pdf				EXOSC10-BGKcLV21-22.pdf	L-EXOSC10-BGKcLV21-22.pdf
ID	2108	2171	2241	2311	2381	7217	2172	2242	2312	2382

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
EXOSC10-BGKcLV21-21_S37_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	448	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1220
EXOSC10-BGKcLV21-21_S37_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	448	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1270
EXOSC10-BGKcLV21-21_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21_S37_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGKcLV21-21_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25213
EXOSC10-BGKcLV21-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21_S37_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGKcLV21-21_S37_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27167
EXOSC10-BGKcLV21-21_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21/Aligned.sortedByCoord.out.bam		ENCORE2	27217
EXOSC10-BGKcLV21-21_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21/Aligned.sortedByCoord.out.bam		ENCORE2	27267
EXOSC10-BGKcLV21-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21/Aligned.sortedByCoord.out.bam		ENCORE2	27317
EXOSC10-BGKcLV21-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	448					GRCh38	V40	EXOSC10-BGKcLV21-21/Aligned.sortedByCoord.out.bam		ENCORE2	27367
EXOSC10-BGKcLV21-22_S38_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	449	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1221
EXOSC10-BGKcLV21-22_S38_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	449	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1271
EXOSC10-BGKcLV21-22_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22_S38_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGKcLV21-22_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25214
EXOSC10-BGKcLV21-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22_S38_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGKcLV21-22_S38_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27168
EXOSC10-BGKcLV21-22_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22/Aligned.sortedByCoord.out.bam		ENCORE2	27218
EXOSC10-BGKcLV21-22_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22/Aligned.sortedByCoord.out.bam		ENCORE2	27268
EXOSC10-BGKcLV21-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22/Aligned.sortedByCoord.out.bam		ENCORE2	27318
EXOSC10-BGKcLV21-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	449					GRCh38	V40	EXOSC10-BGKcLV21-22/Aligned.sortedByCoord.out.bam		ENCORE2	27368