EXOSC2 RNA-Seq in K562

General Information


RBP	EXOSC2
Cell_Line	K562
Method	CRISPR
Exp_Name	EXOSC2-BGKcLV21-K562
ENCODE_series_ID	ENCSR258RES
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR473HXR
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	EXOSC2-BGKcLV21-23
Rep2	EXOSC2-BGKcLV21-24
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	49.7
Rep2_WB	67.8
Antibody Cat#	A303-886A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB374YDD
Status	Released
Project	ENCODE4
ID	68

Experiment Information (Status: Released)

	BGKcLV21-23	BGKcLV21-24
idx	756	757
TRCN#_or_BGC#	BGC#0000517	BGC#0000517
shRNA_or_gRNA_sequence	GAAACATCTAGTGGTGCCGG	GAAACATCTAGTGGTGCCGG
PAM	GGG	GGG
Name	EXOSC2_90	EXOSC2_90
Sample_ID	BGKcLV21-23	BGKcLV21-24
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	EXOSC2	EXOSC2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4089	4273
WB_result	49.7	67.8
Ave_WB	58.8
WB_DONE_date	8/5/20
MW	32.8kDa
IP	Rabbit / I
antibody_Cat#	A303-886A	lot# 1
Antibody DCC ID	ENCAB374YDD
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	4876	4877

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC2	Product_ID: A303-886A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC2-human

Experiment Status

	BGKcLV21-23	BGKcLV21-24
Sample_ID	BGKcLV21-23	BGKcLV21-24
Sample Name
Sample Name	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-24
RBP	EXOSC2	EXOSC2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6127	6128

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-23	BGKcLV21-24
Sample #	45	46
Sample Name	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-24
Sample_Name_Alias
Index Well Position	G05	H05
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	311	307
Peak_Molarity	122.00	98.80
libSampleQC_DNA_Well	DNA_Library_set45/set1/G5.png	DNA_Library_set45/set1/H5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set45/set1/G5.png	RNA_Library_set45/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-23	BGKcLV21-24
RBP	EXOSC2	EXOSC2
Batch_ID	BGKcLV21	BGKcLV21
WB_result	70.100	82.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	819	820

Sequencing Information

	BGKcLV21-23	BGKcLV21-24
Sample_ID	BGKcLV21-23	BGKcLV21-24
Sample Name	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-24
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	143,748,228	82,175,698
total_aligned_reads	134,281,686	72,808,952
unique_aligned_reads	122,837,048	66,621,326
percent_uniqueAligned	0.85453	0.81072
correlation_replicates	0.962135	0.962135
spikein_reads	81,414	46,020
percent_spikeins	0.00057	0.00056
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	450	451

Data Submission Information

	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-24	BGKcLV21-24	BGKcLV21-24	BGKcLV21-24
ENCODE_alias	brenton-graveley:EXOSC2-BGKcLV21	brenton-graveley:EXOSC2-BGKcLV21-23	brenton-graveley:L-EXOSC2-BGKcLV21-23	brenton-graveley:EXOSC2-BGKcLV21-23_S39_R1_001.fastq.gz	brenton-graveley:EXOSC2-BGKcLV21-23_S39_R2_001.fastq.gz	brenton-graveley:EXOSC2-BGKcLV21-K562	brenton-graveley:EXOSC2-BGKcLV21-24	brenton-graveley:L-EXOSC2-BGKcLV21-24	brenton-graveley:EXOSC2-BGKcLV21-24_S40_R1_001.fastq.gz	brenton-graveley:EXOSC2-BGKcLV21-24_S40_R2_001.fastq.gz
ENCODE_accession	ENCSR473HXR	ENCBS047UIY	ENCLB020TZE	ENCFF699SLP	ENCFF300YSS	ENCSR258RES	ENCBS301NYY	ENCLB464AKE	ENCFF799DHS	ENCFF437GLY
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	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-23	BGKcLV21-24	BGKcLV21-24	BGKcLV21-24	BGKcLV21-24
Sample Name	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-23	EXOSC2-BGKcLV21-24	EXOSC2-BGKcLV21-24	EXOSC2-BGKcLV21-24	EXOSC2-BGKcLV21-24
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		EXOSC2-BGKcLV21-23.pdf	L-EXOSC2-BGKcLV21-23.pdf				EXOSC2-BGKcLV21-24.pdf	L-EXOSC2-BGKcLV21-24.pdf
ID	2109	2173	2243	2313	2383	7219	2174	2244	2314	2384

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
EXOSC2-BGKcLV21-23_S39_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	450	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1222
EXOSC2-BGKcLV21-23_S39_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	450	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1272
EXOSC2-BGKcLV21-23_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	450					GRCh38	V40	EXOSC2-BGKcLV21-23_S39_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGKcLV21-23_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25215
EXOSC2-BGKcLV21-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	450					GRCh38	V40	EXOSC2-BGKcLV21-23_S39_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGKcLV21-23_S39_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27169
EXOSC2-BGKcLV21-23_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	450					GRCh38	V40	EXOSC2-BGKcLV21-23/Aligned.sortedByCoord.out.bam		ENCORE2	27219
EXOSC2-BGKcLV21-23_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	450					GRCh38	V40	EXOSC2-BGKcLV21-23/Aligned.sortedByCoord.out.bam		ENCORE2	27269
EXOSC2-BGKcLV21-23_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	450					GRCh38	V40	EXOSC2-BGKcLV21-23/Aligned.sortedByCoord.out.bam		ENCORE2	27319
EXOSC2-BGKcLV21-23_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	450					GRCh38	V40	EXOSC2-BGKcLV21-23/Aligned.sortedByCoord.out.bam		ENCORE2	27369
EXOSC2-BGKcLV21-24_S40_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	451	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1223
EXOSC2-BGKcLV21-24_S40_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	451	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1273
EXOSC2-BGKcLV21-24_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	451					GRCh38	V40	EXOSC2-BGKcLV21-24_S40_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGKcLV21-24_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25216
EXOSC2-BGKcLV21-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	451					GRCh38	V40	EXOSC2-BGKcLV21-24_S40_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGKcLV21-24_S40_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27170
EXOSC2-BGKcLV21-24_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	451					GRCh38	V40	EXOSC2-BGKcLV21-24/Aligned.sortedByCoord.out.bam		ENCORE2	27220
EXOSC2-BGKcLV21-24_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	451					GRCh38	V40	EXOSC2-BGKcLV21-24/Aligned.sortedByCoord.out.bam		ENCORE2	27270
EXOSC2-BGKcLV21-24_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	451					GRCh38	V40	EXOSC2-BGKcLV21-24/Aligned.sortedByCoord.out.bam		ENCORE2	27320
EXOSC2-BGKcLV21-24_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	451					GRCh38	V40	EXOSC2-BGKcLV21-24/Aligned.sortedByCoord.out.bam		ENCORE2	27370