ACTN4 RNA-Seq in K562

General Information


RBP	ACTN4
Cell_Line	K562
Method	CRISPR
Exp_Name	ACTN4-BGKcLV26-K562
ENCODE_series_ID	ENCSR704FXU
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR870TGO
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	ACTN4-BGKcLV26-5
Rep2	ACTN4-BGKcLV26-6
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	44.2
Rep2_qPCR	56.6
Rep1_WB	82.1
Rep2_WB	76.0
Antibody Cat#	A304-768A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB655VCC
Status	Released
Project	ENCODE4
ID	783

Experiment Information (Status: Released)

	BGKcLV26-5	BGKcLV26-6
idx	858	859
TRCN#_or_BGC#	BGC#0000587	BGC#0000587
shRNA_or_gRNA_sequence	GCGAACCAGTCGTACCAGTA	GCGAACCAGTCGTACCAGTA
PAM	CGG	CGG
Name	ACTN4_97	ACTN4_97
Sample_ID	BGKcLV26-5	BGKcLV26-6
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	ACTN4	ACTN4
qPCR_result	44.2	56.6
Ave_qPCR	50.4
RT-qPCR_primer-F	tggtgccagagaaagacagc
RT-qPCR_primer-R	aatcagctctggtctgtgcc
protein_conc	4697	4663
WB_result	82.1	76.0
Ave_WB	79.1
WB_DONE_date	5/18/21	JESS
MW	105KD
IP	Rabbit / I
antibody_Cat#	A304-768A	LOT# 1
Antibody DCC ID	ENCAB655VCC	10/22/21
submitted_to_DCC_date
Rep1_TPM	117.9	0
Rep2_TPM	99.1	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	4990	4991

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ACTN4	Product_ID: A304-768A Lot_ID: 1 Source: Bethyl Labs Target Name: ACTN4-human

Experiment Status

	BGKcLV26-5	BGKcLV26-6
Sample_ID	BGKcLV26-5	BGKcLV26-6
Sample Name
Sample Name	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-6
RBP	ACTN4	ACTN4
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9747	9748

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-5	BGKcLV26-6
Sample #	5	6
Sample Name	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-6
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	266	273
Peak_Molarity	34.20	42.60
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/E1.png	DNA_Library_set48-49/set1/F1.png
RIN	9.2	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/E1.png	RNA_Library_set48-49/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-5	BGKcLV26-6
RBP	ACTN4	ACTN4
Batch_ID	BGKcLV26	BGKcLV26
WB_result	82.100	76.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1564	1565

Sequencing Information

	BGKcLV26-5	BGKcLV26-6
Sample_ID	BGKcLV26-5	BGKcLV26-6
Sample Name	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-6
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	119,411,746	84,728,582
total_aligned_reads	100,681,376	71,637,358
unique_aligned_reads	91,971,474	65,484,704
percent_uniqueAligned	0.77020	0.77288
correlation_replicates	0.999099	0.999099
spikein_reads	47,626	44,738
percent_spikeins	0.00040	0.00053
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1741	1742

Data Submission Information

	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-6	BGKcLV26-6	BGKcLV26-6	BGKcLV26-6
ENCODE_alias	brenton-graveley:ACTN4-BGKcLV26	brenton-graveley:ACTN4-BGKcLV26-5	brenton-graveley:L-ACTN4-BGKcLV26-5	brenton-graveley:ACTN4-BGKcLV26-5_S11_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGKcLV26-5_S11_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGKcLV26-K562	brenton-graveley:ACTN4-BGKcLV26-6	brenton-graveley:L-ACTN4-BGKcLV26-6	brenton-graveley:ACTN4-BGKcLV26-6_S12_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGKcLV26-6_S12_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR870TGO	ENCBS398SEX	ENCLB928WJZ	ENCFF268YAX	ENCFF532LRG	ENCSR704FXU	ENCBS593HDZ	ENCLB410UJO	ENCFF573BMX	ENCFF489YIZ
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	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-5	BGKcLV26-6	BGKcLV26-6	BGKcLV26-6	BGKcLV26-6
Sample Name	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-5	ACTN4-BGKcLV26-6	ACTN4-BGKcLV26-6	ACTN4-BGKcLV26-6	ACTN4-BGKcLV26-6
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		ACTN4-BGKcLV26-5.pdf	L-ACTN4-BGKcLV26-5.pdf				ACTN4-BGKcLV26-6.pdf	L-ACTN4-BGKcLV26-6.pdf
ID	3448	3530	3664	3798	3932	7064	3531	3665	3799	3933

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
ACTN4-BGKcLV26-5_S11_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1741	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3834
ACTN4-BGKcLV26-5_S11_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1741	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3884
ACTN4-BGKcLV26-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5_S11_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGKcLV26-5_S11_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25521
ACTN4-BGKcLV26-5_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5_S11_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGKcLV26-5_S11_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25571
ACTN4-BGKcLV26-5_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5/Aligned.sortedByCoord.out.bam		ENCORE2	26537
ACTN4-BGKcLV26-5_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5/Aligned.sortedByCoord.out.bam		ENCORE2	26587
ACTN4-BGKcLV26-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5/Aligned.sortedByCoord.out.bam		ENCORE2	26637
ACTN4-BGKcLV26-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1741					GRCh38	V40	ACTN4-BGKcLV26-5/Aligned.sortedByCoord.out.bam		ENCORE2	26687
ACTN4-BGKcLV26-6_S12_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1742	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3835
ACTN4-BGKcLV26-6_S12_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1742	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3885
ACTN4-BGKcLV26-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6_S12_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGKcLV26-6_S12_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25522
ACTN4-BGKcLV26-6_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6_S12_L003_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGKcLV26-6_S12_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25572
ACTN4-BGKcLV26-6_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6/Aligned.sortedByCoord.out.bam		ENCORE2	26538
ACTN4-BGKcLV26-6_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6/Aligned.sortedByCoord.out.bam		ENCORE2	26588
ACTN4-BGKcLV26-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6/Aligned.sortedByCoord.out.bam		ENCORE2	26638
ACTN4-BGKcLV26-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1742					GRCh38	V40	ACTN4-BGKcLV26-6/Aligned.sortedByCoord.out.bam		ENCORE2	26688