RAE1 RNA-Seq in K562

General Information


RBP	RAE1
Cell_Line	K562
Method	CRISPR
Exp_Name	RAE1-BGKcLV17-K562
ENCODE_series_ID	ENCSR098LKF
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR092QTF
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	RAE1-BGKcLV17-43
Rep2	RAE1-BGKcLV17-44
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	79.9
Rep2_qPCR	72.5
Rep1_WB	68.9
Rep2_WB	69.3
Antibody Cat#	PA5-76998
Antibody Lot#	lot# TL2693074
Antibody DCC ID	ENCAB079EVO
Status	Released
Project	ENCODE4
ID	92

Experiment Information (Status: Released)

	BGKcLV17-43	BGKcLV17-44
idx	650	651
TRCN#_or_BGC#	BGC#0000394	BGC#0000394
shRNA_or_gRNA_sequence	TTAGCCCACCAACCTTGCCG	TTAGCCCACCAACCTTGCCG
PAM	GGG	GGG
Name	RAE1_91	RAE1_91
Sample_ID	BGKcLV17-43	BGKcLV17-44
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	RAE1	RAE1
qPCR_result	79.9	72.5
Ave_qPCR	76.2
RT-qPCR_primer-F	ATTGCAGGATCATGGGCTAA
RT-qPCR_primer-R	CTGGGCTTTTGGAATGGTCT
protein_conc	5910	5100
WB_result	68.9	69.3
Ave_WB	69.1
WB_DONE_date	7/25/19
MW	41kd
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-76998	lot# TL2693074
Antibody DCC ID	ENCAB079EVO
submitted_to_DCC_date	8/20/19
Rep1_TPM	75.6	0
Rep2_TPM	68	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4768	4769

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RAE1	Product_ID: PA5-76998 Lot_ID: TL2693074 Source: Thermo Fisher Target Name: RAE1-human

Experiment Status

	BGKcLV17-43	BGKcLV17-44
Sample_ID	BGKcLV17-43	BGKcLV17-44
Sample Name
Sample Name	RAE1-BGKcLV17-43	RAE1-BGKcLV17-44
RBP	RAE1	RAE1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5517	5518

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-43	BGKcLV17-44
Sample #	107	108
Sample Name	RAE1-BGKcLV17-43	RAE1-BGKcLV17-44
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-G1	2-H1
Tecan	16.19	29.21
Tecan_date	2019-12-16	2019-12-16
Size_bp	279	265
Peak_Molarity	12.30	23.80
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G9.png	DNA_Library_set43-44/set1/H9.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/G4.png	RNA_Library_set43-44/set4/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-43	BGKcLV17-44
RBP	RAE1	RAE1
Batch_ID	BGKcLV17	BGKcLV17
WB_result	68.900	69.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	683	684

Sequencing Information

	BGKcLV17-43	BGKcLV17-44
Sample_ID	BGKcLV17-43	BGKcLV17-44
Sample Name	RAE1-BGKcLV17-43	RAE1-BGKcLV17-44
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	361,029,940	380,342,354
total_aligned_reads	294,864,234	361,631,136
unique_aligned_reads	268,310,206	327,149,034
percent_uniqueAligned	0.74318	0.86014
correlation_replicates	0.994565	0.994565
spikein_reads	54,404	113,594
percent_spikeins	0.00015	0.00030
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	189	190

Data Submission Information

	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-44	BGKcLV17-44	BGKcLV17-44	BGKcLV17-44
ENCODE_alias	brenton-graveley:RAE1-BGKcLV17	brenton-graveley:RAE1-BGKcLV17-43	brenton-graveley:L-RAE1-BGKcLV17-43	brenton-graveley:RAE1-BGKcLV17-43_S17_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGKcLV17-43_S17_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGKcLV17-K562	brenton-graveley:RAE1-BGKcLV17-44	brenton-graveley:L-RAE1-BGKcLV17-44	brenton-graveley:RAE1-BGKcLV17-44_S18_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGKcLV17-44_S18_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR092QTF	ENCBS750NLG	ENCLB016YAM	ENCFF433VXH	ENCFF095HYT	ENCSR098LKF	ENCBS370MUB	ENCLB241CJZ	ENCFF059PTM	ENCFF074DDP
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	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-43	BGKcLV17-44	BGKcLV17-44	BGKcLV17-44	BGKcLV17-44
Sample Name	RAE1-BGKcLV17-43	RAE1-BGKcLV17-43	RAE1-BGKcLV17-43	RAE1-BGKcLV17-43	RAE1-BGKcLV17-43	RAE1-BGKcLV17-43	RAE1-BGKcLV17-44	RAE1-BGKcLV17-44	RAE1-BGKcLV17-44	RAE1-BGKcLV17-44
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		RAE1-BGKcLV17-43.pdf	L-RAE1-BGKcLV17-43.pdf				RAE1-BGKcLV17-44.pdf	L-RAE1-BGKcLV17-44.pdf
ID	78	236	402	704	734	7297	237	403	705	735

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
RAE1-BGKcLV17-43_S17_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	189	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	291
RAE1-BGKcLV17-43_S17_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	189	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	321
RAE1-BGKcLV17-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43_S17_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGKcLV17-43_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24687
RAE1-BGKcLV17-43_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43/Aligned.sortedByCoord.out.bam		ENCORE2	24717
RAE1-BGKcLV17-43_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43/Aligned.sortedByCoord.out.bam		ENCORE2	24747
RAE1-BGKcLV17-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43/Aligned.sortedByCoord.out.bam		ENCORE2	24777
RAE1-BGKcLV17-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43/Aligned.sortedByCoord.out.bam		ENCORE2	24807
RAE1-BGKcLV17-43_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	189					GRCh38	V40	RAE1-BGKcLV17-43_S17_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGKcLV17-43_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24837
RAE1-BGKcLV17-44_S18_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	190	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	292
RAE1-BGKcLV17-44_S18_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	190	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	322
RAE1-BGKcLV17-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44_S18_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGKcLV17-44_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24688
RAE1-BGKcLV17-44_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44/Aligned.sortedByCoord.out.bam		ENCORE2	24718
RAE1-BGKcLV17-44_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44/Aligned.sortedByCoord.out.bam		ENCORE2	24748
RAE1-BGKcLV17-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44/Aligned.sortedByCoord.out.bam		ENCORE2	24778
RAE1-BGKcLV17-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44/Aligned.sortedByCoord.out.bam		ENCORE2	24808
RAE1-BGKcLV17-44_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	190					GRCh38	V40	RAE1-BGKcLV17-44_S18_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGKcLV17-44_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24838