API5 RNA-Seq in HepG2

General Information


RBP	API5
Cell_Line	HepG2
Method	CRISPR
Exp_Name	API5-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR134POC
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR585MSI
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	API5-BGHcLV27-11
Rep2	API5-BGHcLV27-12
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	50.4
Rep2_qPCR	51.5
Rep1_WB	70.9
Rep2_WB	63.9
Antibody Cat#	A302-784A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB023FOT
Status	Released
Project	ENCODE4
ID	809

Experiment Information (Status: Released)

	BGHcLV27-11	BGHcLV27-12
idx	777	778
TRCN#_or_BGC#	BGC#0000633	BGC#0000633
shRNA_or_gRNA_sequence	TCTCCAGGGTAAAACGGGTG	TCTCCAGGGTAAAACGGGTG
PAM	AGG	AGG
Name	API5_94	API5_94
Sample_ID	BGHcLV27-11	BGHcLV27-12
transduction_Date	5/18/21	5/18/21
days	D6	D6
RBP_name	API5	API5
qPCR_result	50.4	51.5
Ave_qPCR	51.0
RT-qPCR_primer-F	aaattgttggcggagatgag
RT-qPCR_primer-R	ccattttctgcctcttctgg
protein_conc	2662	2953
WB_result	70.9	63.9
Ave_WB	67.4
WB_DONE_date	6/7/21	JESS
MW	59kDa
IP	Rabbit / I
antibody_Cat#	A302-784A	LOT# 2
Antibody DCC ID	ENCAB023FOT	10/22/21
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/03/21	09/03/21
repeat_library
Note
ID	8986	8987

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
API5	Product_ID: A302-784A Lot_ID: 2 Source: Bethyl Labs Target Name: API5-human

Experiment Status

	BGHcLV27-11	BGHcLV27-12
Sample_ID	BGHcLV27-11	BGHcLV27-12
Sample Name
Sample Name	API5-BGHcLV27-11	API5-BGHcLV27-12
RBP	API5	API5
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9681	9682

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-11	BGHcLV27-12
Sample #	85	86
Sample Name	API5-BGHcLV27-11	API5-BGHcLV27-12
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	286	297
Peak_Molarity	124.00	128.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/A8.png	DNA_Library_set48-49/set2/B8.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set48-49/set1/C8.png	RNA_Library_set48-49/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-11	BGHcLV27-12
RBP	API5	API5
Batch_ID	BGHcLV27	BGHcLV27
WB_result	70.900	63.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1644	1645

Sequencing Information

	BGHcLV27-11	BGHcLV27-12
Sample_ID	BGHcLV27-11	BGHcLV27-12
Sample Name	API5-BGHcLV27-11	API5-BGHcLV27-12
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	67,776,610	71,328,984
total_aligned_reads	59,034,472	62,206,998
unique_aligned_reads	55,586,402	58,627,110
percent_uniqueAligned	0.82014	0.82193
correlation_replicates	0.998778	0.998778
spikein_reads	12,042	16,154
percent_spikeins	0.00018	0.00023
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1795	1796

Data Submission Information

	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-12	BGHcLV27-12	BGHcLV27-12	BGHcLV27-12
ENCODE_alias	brenton-graveley:API5-BGHcLV27	brenton-graveley:API5-BGHcLV27-11	brenton-graveley:L-API5-BGHcLV27-11	brenton-graveley:API5-BGHcLV27-11_S65_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGHcLV27-11_S65_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGHcLV27-HepG2	brenton-graveley:API5-BGHcLV27-12	brenton-graveley:L-API5-BGHcLV27-12	brenton-graveley:API5-BGHcLV27-12_S66_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGHcLV27-12_S66_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR585MSI	ENCBS509BGS	ENCLB657PYY	ENCFF540HYJ	ENCFF882VZY	ENCSR134POC	ENCBS026SMB	ENCLB872VUM	ENCFF668PUW	ENCFF073CJW
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	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-11	BGHcLV27-12	BGHcLV27-12	BGHcLV27-12	BGHcLV27-12
Sample Name	API5-BGHcLV27-11	API5-BGHcLV27-11	API5-BGHcLV27-11	API5-BGHcLV27-11	API5-BGHcLV27-11	API5-BGHcLV27-11	API5-BGHcLV27-12	API5-BGHcLV27-12	API5-BGHcLV27-12	API5-BGHcLV27-12
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
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		API5-BGHcLV27-11.pdf	L-API5-BGHcLV27-11.pdf				API5-BGHcLV27-12.pdf	L-API5-BGHcLV27-12.pdf
ID	3437	3508	3642	3776	3910	7088	3509	3643	3777	3911

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
API5-BGHcLV27-11_S65_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1795	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3786
API5-BGHcLV27-11_S65_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1795	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3812
API5-BGHcLV27-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11_S65_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGHcLV27-11_S65_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25473
API5-BGHcLV27-11_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11_S65_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGHcLV27-11_S65_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25499
API5-BGHcLV27-11_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11/Aligned.sortedByCoord.out.bam		ENCORE2	26437
API5-BGHcLV27-11_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11/Aligned.sortedByCoord.out.bam		ENCORE2	26463
API5-BGHcLV27-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11/Aligned.sortedByCoord.out.bam		ENCORE2	26489
API5-BGHcLV27-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1795					GRCh38	V40	API5-BGHcLV27-11/Aligned.sortedByCoord.out.bam		ENCORE2	26515
API5-BGHcLV27-12_S66_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1796	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3787
API5-BGHcLV27-12_S66_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1796	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3813
API5-BGHcLV27-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12_S66_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGHcLV27-12_S66_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25474
API5-BGHcLV27-12_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12_S66_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGHcLV27-12_S66_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25500
API5-BGHcLV27-12_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12/Aligned.sortedByCoord.out.bam		ENCORE2	26438
API5-BGHcLV27-12_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12/Aligned.sortedByCoord.out.bam		ENCORE2	26464
API5-BGHcLV27-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12/Aligned.sortedByCoord.out.bam		ENCORE2	26490
API5-BGHcLV27-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1796					GRCh38	V40	API5-BGHcLV27-12/Aligned.sortedByCoord.out.bam		ENCORE2	26516