RANGAP1 RNA-Seq in HepG2

General Information


RBP	RANGAP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RANGAP1-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	RANGAP1-BGHcLV45-53
Rep2	RANGAP1-BGHcLV45-54
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	64.8
Rep2_WB	65.5
Antibody Cat#	36067S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1625

Experiment Information (Status: Submitting)

	BGHcLV45-53	BGHcLV45-54
idx	1217	1217
TRCN#_or_BGC#	BGC#0001048	BGC#0001048
shRNA_or_gRNA_sequence	GCCAAGACTCAGGTGGCCGG	GCCAAGACTCAGGTGGCCGG
PAM	ggg	ggg
Name	RANGAP1_82	RANGAP1_82
Sample_ID	BGHcLV45-53	BGHcLV45-54
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	RANGAP1	RANGAP1
qPCR_result	0.0	0.0
Ave_qPCR
RT-qPCR_primer-F	GGTGGTCTCTGCCTTCCTAAAG
RT-qPCR_primer-R	CGAGGAGTTGAAAGCCTTCTGC
protein_conc	3453	3557
WB_result	64.8	65.5
Ave_WB
WB_DONE_date	10/18/24
MW	82KD
IP
antibody_Cat#	36067S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9743	9744

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RANGAP1	Product_ID: 36067S Lot_ID: 1 Source: Cell Signaling Technology Target Name: RANGAP1-human

Experiment Status

	BGHcLV45-53	BGHcLV45-54
Sample_ID	BGHcLV45-53	BGHcLV45-54
Sample Name
Sample Name	RANGAP1-BGHcLV45-53	RANGAP1-BGHcLV45-54
RBP	RANGAP1	RANGAP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13708	13709

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-53	BGHcLV45-54
Sample #	23	24
Sample Name	RANGAP1-BGHcLV45-53	RANGAP1-BGHcLV45-54
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	286	284
Peak_Molarity	72.70	52.30
libSampleQC_DNA_Well	DNA_Library_set76/set1/G9.png	DNA_Library_set76/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/G3.png	RNA_Library_set76/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-53	BGHcLV45-54
RBP	RANGAP1	RANGAP1
Batch_ID	BGHcLV45	BGHcLV45
WB_result	64.800	65.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4632	4633

Sequencing Information

	BGHcLV45-53	BGHcLV45-54
Sample_ID	BGHcLV45-53	BGHcLV45-54
Sample Name	RANGAP1-BGHcLV45-53	RANGAP1-BGHcLV45-54
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	43,843,329	39,375,712
total_aligned_reads	38,757,399	33,775,682
unique_aligned_reads	36,425,874	31,696,250
percent_uniqueAligned	0.83082	0.80497
correlation_replicates	0.997647	0.997647
spikein_reads	24,922	46,776
percent_spikeins	0.00057	0.00119
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3343	3344

Data Submission Information DCC submission information was not avaliable

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
RANGAP1-BGHcLV45-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3343	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31834
RANGAP1-BGHcLV45-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3343	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31876
RANGAP1-BGHcLV45-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGHcLV45-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31918
RANGAP1-BGHcLV45-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_Aligned.sortedByCoord.out.bam		ENCORE2	31960
RANGAP1-BGHcLV45-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_Aligned.sortedByCoord.out.bam		ENCORE2	32002
RANGAP1-BGHcLV45-53_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_Aligned.sortedByCoord.out.bam		ENCORE2	32044
RANGAP1-BGHcLV45-53_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_Aligned.sortedByCoord.out.bam		ENCORE2	32086
RANGAP1-BGHcLV45-53_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3343					GRCh38	V40	RANGAP1-BGHcLV45-53_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGHcLV45-53_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32128
RANGAP1-BGHcLV45-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3344	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31835
RANGAP1-BGHcLV45-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3344	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31877
RANGAP1-BGHcLV45-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGHcLV45-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31919
RANGAP1-BGHcLV45-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_Aligned.sortedByCoord.out.bam		ENCORE2	31961
RANGAP1-BGHcLV45-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_Aligned.sortedByCoord.out.bam		ENCORE2	32003
RANGAP1-BGHcLV45-54_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_Aligned.sortedByCoord.out.bam		ENCORE2	32045
RANGAP1-BGHcLV45-54_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_Aligned.sortedByCoord.out.bam		ENCORE2	32087
RANGAP1-BGHcLV45-54_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3344					GRCh38	V40	RANGAP1-BGHcLV45-54_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,RANGAP1-BGHcLV45-54_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32129