ACTN4 RNA-Seq in HepG2

General Information


RBP	ACTN4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ACTN4-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR942QWP
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR029LLJ
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	ACTN4-BGHcLV25-5
Rep2	ACTN4-BGHcLV25-6
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	82.1
Rep2_WB	79.6
Antibody Cat#	A304-768A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB655VCC
Status	Released
Project	ENCODE4
ID	13

Experiment Information (Status: Released)

	BGHcLV25-5	BGHcLV25-6
idx	712	713
TRCN#_or_BGC#	BGC#0000587	BGC#0000587
shRNA_or_gRNA_sequence	GCGAACCAGTCGTACCAGTA	GCGAACCAGTCGTACCAGTA
PAM	CGG	CGG
Name	ACTN4_97	ACTN4_97
Sample_ID	BGHcLV25-5	BGHcLV25-6
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	ACTN4	ACTN4
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tggtgccagagaaagacagc
RT-qPCR_primer-R	aatcagctctggtctgtgcc
protein_conc	4688	3604
WB_result	82.1	79.6
Ave_WB	80.9
WB_DONE_date	4/7/21	JESS
MW	105KD
IP	Rabbit / I
antibody_Cat#	A304-768A	LOT# 1
Antibody DCC ID	ENCAB655VCC
submitted_to_DCC_date	10/26/21
Rep1_TPM	430	0
Rep2_TPM	213	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6867	6868

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

	BGHcLV25-5	BGHcLV25-6
Sample_ID	BGHcLV25-5	BGHcLV25-6
Sample Name
Sample Name	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-6
RBP	ACTN4	ACTN4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7831	7832

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-5	BGHcLV25-6
Sample #	29	30
Sample Name	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-6
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-06-04	2021-06-04
Lib_ID	Lib-210604	Lib-210604
Tecan_Location
Tecan
Tecan_date
Size_bp	304	309
Peak_Molarity	74.20	74.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/E7.png	DNA_Library_set47/set1/F7.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set47/set1/E4.png	RNA_Library_set47/set1/F4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-5	BGHcLV25-6
RBP	ACTN4	ACTN4
Batch_ID	BGHcLV25	BGHcLV25
WB_result	82.100	79.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1492	1493

Sequencing Information

	BGHcLV25-5	BGHcLV25-6
Sample_ID	BGHcLV25-5	BGHcLV25-6
Sample Name	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-6
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	112,096,748	102,135,098
total_aligned_reads	103,805,910	94,635,156
unique_aligned_reads	97,871,424	89,276,600
percent_uniqueAligned	0.87310	0.87410
correlation_replicates	0.999572	0.999572
spikein_reads	29,906	23,594
percent_spikeins	0.00027	0.00023
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	574	575

Data Submission Information

	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-6	BGHcLV25-6	BGHcLV25-6	BGHcLV25-6
ENCODE_alias	brenton-graveley:ACTN4-BGHcLV25	brenton-graveley:ACTN4-BGHcLV25-5	brenton-graveley:L-ACTN4-BGHcLV25-5	brenton-graveley:ACTN4-BGHcLV25-5_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGHcLV25-5_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGHcLV25-HepG2	brenton-graveley:ACTN4-BGHcLV25-6	brenton-graveley:L-ACTN4-BGHcLV25-6	brenton-graveley:ACTN4-BGHcLV25-6_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ACTN4-BGHcLV25-6_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR029LLJ	ENCBS395IEJ	ENCLB584ULM	ENCFF310XWV	ENCFF517SIN	ENCSR942QWP	ENCBS887WYP	ENCLB185LWB	ENCFF742EYW	ENCFF922SDP
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	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-5	BGHcLV25-6	BGHcLV25-6	BGHcLV25-6	BGHcLV25-6
Sample Name	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-5	ACTN4-BGHcLV25-6	ACTN4-BGHcLV25-6	ACTN4-BGHcLV25-6	ACTN4-BGHcLV25-6
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2021-11-04	2022-03-02	2021-11-04	2021-11-04	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV47_biosample_protocol	LV47_library_protocol				LV47_biosample_protocol	LV47_library_protocol
protocol_URL		ACTN4-BGHcLV25-5.pdf	L-ACTN4-BGHcLV25-5.pdf				ACTN4-BGHcLV25-6.pdf	L-ACTN4-BGHcLV25-6.pdf
ID	3249	3285	3329	3373	3417	7063	3286	3330	3374	3418

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-BGHcLV25-5_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	574	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3692
ACTN4-BGHcLV25-5_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	574	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3738
ACTN4-BGHcLV25-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGHcLV25-5_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25381
ACTN4-BGHcLV25-5_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGHcLV25-5_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25425
ACTN4-BGHcLV25-5_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5/Aligned.sortedByCoord.out.bam		ENCORE2	26257
ACTN4-BGHcLV25-5_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5/Aligned.sortedByCoord.out.bam		ENCORE2	26301
ACTN4-BGHcLV25-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5/Aligned.sortedByCoord.out.bam		ENCORE2	26345
ACTN4-BGHcLV25-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	574					GRCh38	V40	ACTN4-BGHcLV25-5/Aligned.sortedByCoord.out.bam		ENCORE2	26389
ACTN4-BGHcLV25-6_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	575	NovaSeq6000	100	paired-ended	1				NT-BGHcLV25-1_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3693
ACTN4-BGHcLV25-6_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	575	NovaSeq6000	100	paired-ended	2				NT-BGHcLV25-1_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV25-2_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3739
ACTN4-BGHcLV25-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGHcLV25-6_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25382
ACTN4-BGHcLV25-6_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,ACTN4-BGHcLV25-6_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25426
ACTN4-BGHcLV25-6_Signal.Unique.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6/Aligned.sortedByCoord.out.bam		ENCORE2	26258
ACTN4-BGHcLV25-6_Signal.Unique.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6/Aligned.sortedByCoord.out.bam		ENCORE2	26302
ACTN4-BGHcLV25-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6/Aligned.sortedByCoord.out.bam		ENCORE2	26346
ACTN4-BGHcLV25-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	575					GRCh38	V40	ACTN4-BGHcLV25-6/Aligned.sortedByCoord.out.bam		ENCORE2	26390