CACTIN RNA-Seq in HepG2

General Information


RBP	CACTIN
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CACTIN-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR342PHP
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR865WQR
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	CACTIN-BGHcLV22-3
Rep2	CACTIN-BGHcLV22-4
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	56.2
Rep2_WB	57.9
Antibody Cat#	A303-349A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB389VTI
Status	Released
Project	ENCODE4
ID	37

Experiment Information (Status: Released)

	BGHcLV22-3	BGHcLV22-4
idx	596	597
TRCN#_or_BGC#	BGC#0000495	BGC#0000495
shRNA_or_gRNA_sequence	ACGCCGGCAGGTACAGCCCG	ACGCCGGCAGGTACAGCCCG
PAM	CGG	CGG
Name	CACTIN_85	CACTIN_85
Sample_ID	BGHcLV22-3	BGHcLV22-4
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	CACTIN	CACTIN
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GGACGAGATCTCCAAGCTCC
RT-qPCR_primer-R	TTGAACACCGACTGCACATC
protein_conc	2374	1634
WB_result	56.2	57.9
Ave_WB	57.1
WB_DONE_date	8/31/20	JESS
MW	88.7kDa
IP	Rabbit / I
antibody_Cat#	A303-349A	Lot# 1
Antibody DCC ID	ENCAB389VTI
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6751	6752

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CACTIN	Product_ID: A303-349A Lot_ID: 1 Source: Bethyl Labs Target Name: CACTIN-human

Experiment Status

	BGHcLV22-3	BGHcLV22-4
Sample_ID	BGHcLV22-3	BGHcLV22-4
Sample Name
Sample Name	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-4
RBP	CACTIN	CACTIN
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7367	7368

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-3	BGHcLV22-4
Sample #	3	4
Sample Name	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	292	292
Peak_Molarity	239.00	91.50
libSampleQC_DNA_Well	DNA_Library_set46/set1/C1.png	DNA_Library_set46/set1/D1.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set46/set1/C9.png	RNA_Library_set46/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-3	BGHcLV22-4
RBP	CACTIN	CACTIN
Batch_ID	BGHcLV22	BGHcLV22
WB_result	56.200	57.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1378	1379

Sequencing Information

	BGHcLV22-3	BGHcLV22-4
Sample_ID	BGHcLV22-3	BGHcLV22-4
Sample Name	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-4
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	157,227,186	227,715,310
total_aligned_reads	129,656,554	192,372,704
unique_aligned_reads	121,083,840	179,830,026
percent_uniqueAligned	0.77012	0.78971
correlation_replicates	0.999654	0.999654
spikein_reads	93,956	89,070
percent_spikeins	0.00060	0.00039
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	484	485

Data Submission Information

	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-4	BGHcLV22-4	BGHcLV22-4	BGHcLV22-4
ENCODE_alias	brenton-graveley:CACTIN-BGHcLV22	brenton-graveley:CACTIN-BGHcLV22-3	brenton-graveley:L-CACTIN-BGHcLV22-3	brenton-graveley:CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGHcLV22-HepG2	brenton-graveley:CACTIN-BGHcLV22-4	brenton-graveley:L-CACTIN-BGHcLV22-4	brenton-graveley:CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR865WQR	ENCBS503ZTZ	ENCLB320XJO	ENCFF218XGI	ENCFF713QMR	ENCSR342PHP	ENCBS314YFX	ENCLB089OMY	ENCFF233LCM	ENCFF686XKK
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	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-3	BGHcLV22-4	BGHcLV22-4	BGHcLV22-4	BGHcLV22-4
Sample Name	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-3	CACTIN-BGHcLV22-4	CACTIN-BGHcLV22-4	CACTIN-BGHcLV22-4	CACTIN-BGHcLV22-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-06-02	2022-02-04	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2022-02-04	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		CACTIN-BGHcLV22-3.pdf	L-CACTIN-BGHcLV22-3.pdf				CACTIN-BGHcLV22-4.pdf	L-CACTIN-BGHcLV22-4.pdf
ID	2396	2429	2493	2557	2587	7108	2430	2494	2558	2588

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
CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	484	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1348
CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	484	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1412
CACTIN-BGHcLV22-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25251
CACTIN-BGHcLV22-3_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGHcLV22-3_GGACTTGG+CGTCTGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25349
CACTIN-BGHcLV22-3_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3/Aligned.sortedByCoord.out.bam		ENCORE2	25999
CACTIN-BGHcLV22-3_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3/Aligned.sortedByCoord.out.bam		ENCORE2	26029
CACTIN-BGHcLV22-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3/Aligned.sortedByCoord.out.bam		ENCORE2	26059
CACTIN-BGHcLV22-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	484					GRCh38	V40	CACTIN-BGHcLV22-3/Aligned.sortedByCoord.out.bam		ENCORE2	26089
CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	485	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1349
CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	485	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1413
CACTIN-BGHcLV22-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25252
CACTIN-BGHcLV22-4_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGHcLV22-4_AAGTCCAA+TACTCATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25350
CACTIN-BGHcLV22-4_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4/Aligned.sortedByCoord.out.bam		ENCORE2	26000
CACTIN-BGHcLV22-4_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4/Aligned.sortedByCoord.out.bam		ENCORE2	26030
CACTIN-BGHcLV22-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4/Aligned.sortedByCoord.out.bam		ENCORE2	26060
CACTIN-BGHcLV22-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	485					GRCh38	V40	CACTIN-BGHcLV22-4/Aligned.sortedByCoord.out.bam		ENCORE2	26090