RAE1 RNA-Seq in HepG2

General Information


RBP	RAE1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RAE1-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR898VIA
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR723QPD
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	RAE1-BGHcLV18-39
Rep2	RAE1-BGHcLV18-40
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	71.1
Rep2_qPCR	75.0
Rep1_WB	61.5
Rep2_WB	68.3
Antibody Cat#	PA5-76998
Antibody Lot#	lot# TL2693074
Antibody DCC ID	ENCAB079EVO
Status	Released
Project	ENCODE4
ID	115

Experiment Information (Status: Released)

	BGHcLV18-39	BGHcLV18-40
idx	532	533
TRCN#_or_BGC#	BGC#0000394	BGC#0000394
shRNA_or_gRNA_sequence	TTAGCCCACCAACCTTGCCG	TTAGCCCACCAACCTTGCCG
PAM	GGG	GGG
Name	RAE1_91	RAE1_91
Sample_ID	BGHcLV18-39	BGHcLV18-40
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	RAE1	RAE1
qPCR_result	71.1	75.0
Ave_qPCR	73.1
RT-qPCR_primer-F	ATTGCAGGATCATGGGCTAA
RT-qPCR_primer-R	CTGGGCTTTTGGAATGGTCT
protein_conc	3968	3258
WB_result	61.5	68.3
Ave_WB	64.9
WB_DONE_date	8/21/19
MW	41kd
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-76998	lot# TL2693074
Antibody DCC ID	ENCAB079EVO
submitted_to_DCC_date
Rep1_TPM	82	0
Rep2_TPM	84	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6687	6688

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

	BGHcLV18-39	BGHcLV18-40
Sample_ID	BGHcLV18-39	BGHcLV18-40
Sample Name
Sample Name	RAE1-BGHcLV18-39	RAE1-BGHcLV18-40
RBP	RAE1	RAE1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5647	5648

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-39	BGHcLV18-40
Sample #	153	154
Sample Name	RAE1-BGHcLV18-39	RAE1-BGHcLV18-40
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	5-E1	5-F1
Tecan	39.83	33.37
Tecan_date	2019-12-16	2019-12-16
Size_bp	265	268
Peak_Molarity	29.90	30.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G8.png	DNA_Library_set43-44/set2/H8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set43-44/set4/C10.png	RNA_Library_set43-44/set4/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-39	BGHcLV18-40
RBP	RAE1	RAE1
Batch_ID	BGHcLV18	BGHcLV18
WB_result	61.500	68.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	729	730

Sequencing Information

	BGHcLV18-39	BGHcLV18-40
Sample_ID	BGHcLV18-39	BGHcLV18-40
Sample Name	RAE1-BGHcLV18-39	RAE1-BGHcLV18-40
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	220,360,292	137,654,088
total_aligned_reads	211,088,258	123,750,204
unique_aligned_reads	197,404,442	115,736,494
percent_uniqueAligned	0.89583	0.84078
correlation_replicates	0.999034	0.999034
spikein_reads	358,940	221,486
percent_spikeins	0.00163	0.00161
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	235	236

Data Submission Information

	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-40	BGHcLV18-40	BGHcLV18-40	BGHcLV18-40
ENCODE_alias	brenton-graveley:RAE1-BGHcLV18	brenton-graveley:RAE1-BGHcLV18-39	brenton-graveley:L-RAE1-BGHcLV18-39	brenton-graveley:RAE1-BGHcLV18-39_S65_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGHcLV18-39_S65_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGHcLV18-HepG2	brenton-graveley:RAE1-BGHcLV18-40	brenton-graveley:L-RAE1-BGHcLV18-40	brenton-graveley:RAE1-BGHcLV18-40_S66_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RAE1-BGHcLV18-40_S66_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR723QPD	ENCBS963YGC	ENCLB136VWB	ENCFF233HNP	ENCFF877OCU	ENCSR898VIA	ENCBS244PIB	ENCLB094QTX	ENCFF218TKQ	ENCFF842CWT
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	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-39	BGHcLV18-40	BGHcLV18-40	BGHcLV18-40	BGHcLV18-40
Sample Name	RAE1-BGHcLV18-39	RAE1-BGHcLV18-39	RAE1-BGHcLV18-39	RAE1-BGHcLV18-39	RAE1-BGHcLV18-39	RAE1-BGHcLV18-39	RAE1-BGHcLV18-40	RAE1-BGHcLV18-40	RAE1-BGHcLV18-40	RAE1-BGHcLV18-40
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		RAE1-BGHcLV18-39.pdf	L-RAE1-BGHcLV18-39.pdf				RAE1-BGHcLV18-40.pdf	L-RAE1-BGHcLV18-40.pdf
ID	62	204	370	620	672	7296	205	371	621	673

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-BGHcLV18-39_S65_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	235	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	207
RAE1-BGHcLV18-39_S65_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	235	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	259
RAE1-BGHcLV18-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39_S65_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGHcLV18-39_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24927
RAE1-BGHcLV18-39_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39/Aligned.sortedByCoord.out.bam		ENCORE2	24979
RAE1-BGHcLV18-39_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39/Aligned.sortedByCoord.out.bam		ENCORE2	25031
RAE1-BGHcLV18-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39/Aligned.sortedByCoord.out.bam		ENCORE2	25083
RAE1-BGHcLV18-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39/Aligned.sortedByCoord.out.bam		ENCORE2	25135
RAE1-BGHcLV18-39_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	235					GRCh38	V40	RAE1-BGHcLV18-39_S65_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGHcLV18-39_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25187
RAE1-BGHcLV18-40_S66_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	236	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	208
RAE1-BGHcLV18-40_S66_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	236	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	260
RAE1-BGHcLV18-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40_S66_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGHcLV18-40_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24928
RAE1-BGHcLV18-40_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40/Aligned.sortedByCoord.out.bam		ENCORE2	24980
RAE1-BGHcLV18-40_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40/Aligned.sortedByCoord.out.bam		ENCORE2	25032
RAE1-BGHcLV18-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40/Aligned.sortedByCoord.out.bam		ENCORE2	25084
RAE1-BGHcLV18-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40/Aligned.sortedByCoord.out.bam		ENCORE2	25136
RAE1-BGHcLV18-40_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	236					GRCh38	V40	RAE1-BGHcLV18-40_S66_R1_001.filtered.trimmed.paired.fastq.gz,RAE1-BGHcLV18-40_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25188