CACTIN RNA-Seq in K562

General Information


RBP	CACTIN
Cell_Line	K562
Method	CRISPR
Exp_Name	CACTIN-BGKcLV23-K562
ENCODE_series_ID	ENCSR238CFL
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR416WTE
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	CACTIN-BGKcLV23-27
Rep2	CACTIN-BGKcLV23-28
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	11.0
Rep2_qPCR	0.0
Rep1_WB	61.8
Rep2_WB	53.6
Antibody Cat#	A303-349A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB389VTI
Status	Released
Project	ENCODE4
ID	26

Experiment Information (Status: Released)

	BGKcLV23-27	BGKcLV23-28
idx	813	814
TRCN#_or_BGC#	BGC#0000495	BGC#0000495
shRNA_or_gRNA_sequence	ACGCCGGCAGGTACAGCCCG	ACGCCGGCAGGTACAGCCCG
PAM	CGG	CGG
Name	CACTIN_85	CACTIN_85
Sample_ID	BGKcLV23-27	BGKcLV23-28
transduction_Date	9/17/20	9/17/20
days	Day 6	Day 6
RBP_name	CACTIN	CACTIN
qPCR_result	11.0	0.0
Ave_qPCR	5.5
RT-qPCR_primer-F	GGACGAGATCTCCAAGCTCC
RT-qPCR_primer-R	TTGAACACCGACTGCACATC
protein_conc	3118	3103
WB_result	61.8	53.6
Ave_WB	57.7
WB_DONE_date	10/26/20
MW	88.7KD
IP	Rabbit / I
antibody_Cat#	A303-349A	LOT# 1
Antibody DCC ID	ENCAB389VTI
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	4933	4934

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

	BGKcLV23-27	BGKcLV23-28
Sample_ID	BGKcLV23-27	BGKcLV23-28
Sample Name
Sample Name	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-28
RBP	CACTIN	CACTIN
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7441	7442

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-27	BGKcLV23-28
Sample #	43	44
Sample Name	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-28
Sample_Name_Alias
Index Well Position	C06	D06
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	295	291
Peak_Molarity	197.00	101.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C6.png	DNA_Library_set46/set1/D6.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_set46/set2/C10.png	RNA_Library_set46/set2/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-27	BGKcLV23-28
RBP	CACTIN	CACTIN
Batch_ID	BGKcLV23	BGKcLV23
WB_result	61.800	53.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1418	1419

Sequencing Information

	BGKcLV23-27	BGKcLV23-28
Sample_ID	BGKcLV23-27	BGKcLV23-28
Sample Name	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-28
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	200,386,294	256,616,104
total_aligned_reads	183,828,222	233,572,332
unique_aligned_reads	167,687,216	211,736,964
percent_uniqueAligned	0.83682	0.82511
correlation_replicates	0.997648	0.997648
spikein_reads	90,964	86,284
percent_spikeins	0.00045	0.00034
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	524	525

Data Submission Information

	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-28	BGKcLV23-28	BGKcLV23-28	BGKcLV23-28
ENCODE_alias	brenton-graveley:CACTIN-BGKcLV23	brenton-graveley:CACTIN-BGKcLV23-27	brenton-graveley:L-CACTIN-BGKcLV23-27	brenton-graveley:CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGKcLV23-K562	brenton-graveley:CACTIN-BGKcLV23-28	brenton-graveley:L-CACTIN-BGKcLV23-28	brenton-graveley:CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR416WTE	ENCBS763TFO	ENCLB856FIO	ENCFF977JGY	ENCFF974JLT	ENCSR238CFL	ENCBS996KHM	ENCLB923TMV	ENCFF306BSL	ENCFF669HGJ
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	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-27	BGKcLV23-28	BGKcLV23-28	BGKcLV23-28	BGKcLV23-28
Sample Name	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-27	CACTIN-BGKcLV23-28	CACTIN-BGKcLV23-28	CACTIN-BGKcLV23-28	CACTIN-BGKcLV23-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		CACTIN-BGKcLV23-27.pdf	L-CACTIN-BGKcLV23-27.pdf				CACTIN-BGKcLV23-28.pdf	L-CACTIN-BGKcLV23-28.pdf
ID	2416	2469	2533	2627	2661	7109	2470	2534	2628	2662

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-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	524	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1388
CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	524	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1452
CACTIN-BGKcLV23-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25291
CACTIN-BGKcLV23-27_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGKcLV23-27_AAGATACT+ATGTAAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25325
CACTIN-BGKcLV23-27_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27/Aligned.sortedByCoord.out.bam		ENCORE2	26129
CACTIN-BGKcLV23-27_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27/Aligned.sortedByCoord.out.bam		ENCORE2	26163
CACTIN-BGKcLV23-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27/Aligned.sortedByCoord.out.bam		ENCORE2	26197
CACTIN-BGKcLV23-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	524					GRCh38	V40	CACTIN-BGKcLV23-27/Aligned.sortedByCoord.out.bam		ENCORE2	26231
CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	525	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1389
CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	525	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1453
CACTIN-BGKcLV23-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25292
CACTIN-BGKcLV23-28_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,CACTIN-BGKcLV23-28_GGAGCGTC+GCACGGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25326
CACTIN-BGKcLV23-28_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28/Aligned.sortedByCoord.out.bam		ENCORE2	26130
CACTIN-BGKcLV23-28_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28/Aligned.sortedByCoord.out.bam		ENCORE2	26164
CACTIN-BGKcLV23-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28/Aligned.sortedByCoord.out.bam		ENCORE2	26198
CACTIN-BGKcLV23-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	525					GRCh38	V40	CACTIN-BGKcLV23-28/Aligned.sortedByCoord.out.bam		ENCORE2	26232