AGFG1 RNA-Seq in HepG2

General Information


RBP	AGFG1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	AGFG1-BGHcLV25-HepG2
ENCODE_series_ID	ENCSR241PEK
Batch_ID	BGHcLV25
Pool ID	Pool-210622
Local_Set_Name	set47
ENCODE_KD_Exp_ID	ENCSR892ZGW
ENCODE_CN_Exp_ID	ENCSR953VMB
Rep1	AGFG1-BGHcLV25-19
Rep2	AGFG1-BGHcLV25-20
CN1	NT-BGHcLV25-1
CN2	NT-BGHcLV25-2
Rep1_qPCR	32.2
Rep2_qPCR	31.1
Rep1_WB	96.2
Rep2_WB	96.8
Antibody Cat#	A301-792A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB794UUE
Status	Released
Project	ENCODE4
ID	17

Experiment Information (Status: Released)

	BGHcLV25-19	BGHcLV25-20
idx	726	727
TRCN#_or_BGC#	BGC#0000600	BGC#0000600
shRNA_or_gRNA_sequence	GACCGTCATGTTAACGTAGG	GACCGTCATGTTAACGTAGG
PAM	TGG	TGG
Name	AGFG1_97	AGFG1_97
Sample_ID	BGHcLV25-19	BGHcLV25-20
transduction_Date	2/18/21	2/18/21
days	D6	D6
RBP_name	AGFG1	AGFG1
qPCR_result	32.2	31.1
Ave_qPCR	31.7
RT-qPCR_primer-F	tagtttggggctgaaaagga
RT-qPCR_primer-R	gctccagctcctcagtcaac
protein_conc	4984	5342
WB_result	96.2	96.8
Ave_WB	96.5
WB_DONE_date	5/26/21	JESS
MW	58KD
IP	Rabbit / I
antibody_Cat#	A301-792A	LOT# 1
Antibody DCC ID	ENCAB794UUE
submitted_to_DCC_date	10/26/21
Rep1_TPM	80	0
Rep2_TPM	100	0
Action	Ready	Ready
Library_start_date	06/16/21	06/16/21
repeat_library
Note
ID	6885	6886

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
AGFG1	Product_ID: A301-792A Lot_ID: 1 Source: Bethyl Labs Target Name: AGFG1-human

Experiment Status

	BGHcLV25-19	BGHcLV25-20
Sample_ID	BGHcLV25-19	BGHcLV25-20
Sample Name
Sample Name	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-20
RBP	AGFG1	AGFG1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-04	2021-11-04
Project	ENCODE4	ENCODE4
Note
ID	7839	7840

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV25-19	BGHcLV25-20
Sample #	37	38
Sample Name	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-20
Sample_Name_Alias
Index Well Position	E11	F11
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	302	316
Peak_Molarity	70.20	70.10
libSampleQC_DNA_Well	DNA_Library_set47/set1/E8.png	DNA_Library_set47/set1/F8.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set47/set2/F6.png	RNA_Library_set47/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-06-22	2021-06-22
Sample_ID	BGHcLV25-19	BGHcLV25-20
RBP	AGFG1	AGFG1
Batch_ID	BGHcLV25	BGHcLV25
WB_result	96.200	96.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1500	1501

Sequencing Information

	BGHcLV25-19	BGHcLV25-20
Sample_ID	BGHcLV25-19	BGHcLV25-20
Sample Name	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-20
Pool ID	Pool-210622	Pool-210622
LocalServer_folder	set47	set47
total_reads	120,250,998	119,347,310
total_aligned_reads	112,660,698	112,721,174
unique_aligned_reads	106,128,290	106,191,624
percent_uniqueAligned	0.88256	0.88977
correlation_replicates	0.997195	0.997195
spikein_reads	25,970	29,302
percent_spikeins	0.00022	0.00025
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	582	583

Data Submission Information

	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-20	BGHcLV25-20	BGHcLV25-20	BGHcLV25-20
ENCODE_alias	brenton-graveley:AGFG1-BGHcLV25	brenton-graveley:AGFG1-BGHcLV25-19	brenton-graveley:L-AGFG1-BGHcLV25-19	brenton-graveley:AGFG1-BGHcLV25-19_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGHcLV25-19_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGHcLV25-HepG2	brenton-graveley:AGFG1-BGHcLV25-20	brenton-graveley:L-AGFG1-BGHcLV25-20	brenton-graveley:AGFG1-BGHcLV25-20_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGHcLV25-20_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR892ZGW	ENCBS512NDV	ENCLB610FNQ	ENCFF022VGK	ENCFF267YET	ENCSR241PEK	ENCBS671GNG	ENCLB556RJM	ENCFF109VOJ	ENCFF225EPD
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	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-19	BGHcLV25-20	BGHcLV25-20	BGHcLV25-20	BGHcLV25-20
Sample Name	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-19	AGFG1-BGHcLV25-20	AGFG1-BGHcLV25-20	AGFG1-BGHcLV25-20	AGFG1-BGHcLV25-20
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		AGFG1-BGHcLV25-19.pdf	L-AGFG1-BGHcLV25-19.pdf				AGFG1-BGHcLV25-20.pdf	L-AGFG1-BGHcLV25-20.pdf
ID	3253	3293	3337	3381	3425	7072	3294	3338	3382	3426

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
AGFG1-BGHcLV25-19_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	582	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	3702
AGFG1-BGHcLV25-19_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	582	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	3748
AGFG1-BGHcLV25-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	582					GRCh38	V40	AGFG1-BGHcLV25-19_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGHcLV25-19_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25391
AGFG1-BGHcLV25-19_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	582					GRCh38	V40	AGFG1-BGHcLV25-19_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGHcLV25-19_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25435
AGFG1-BGHcLV25-19_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	582					GRCh38	V40	AGFG1-BGHcLV25-19/Aligned.sortedByCoord.out.bam		ENCORE2	26267
AGFG1-BGHcLV25-19_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	582					GRCh38	V40	AGFG1-BGHcLV25-19/Aligned.sortedByCoord.out.bam		ENCORE2	26311
AGFG1-BGHcLV25-19_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	582					GRCh38	V40	AGFG1-BGHcLV25-19/Aligned.sortedByCoord.out.bam		ENCORE2	26355
AGFG1-BGHcLV25-19_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	582					GRCh38	V40	AGFG1-BGHcLV25-19/Aligned.sortedByCoord.out.bam		ENCORE2	26399
AGFG1-BGHcLV25-20_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	583	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	3703
AGFG1-BGHcLV25-20_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set47/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	583	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	3749
AGFG1-BGHcLV25-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set47/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	583					GRCh38	V40	AGFG1-BGHcLV25-20_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGHcLV25-20_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25392
AGFG1-BGHcLV25-20_quant.sf	ENCODE_DATA/set47/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	583					GRCh38	V40	AGFG1-BGHcLV25-20_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGHcLV25-20_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25436
AGFG1-BGHcLV25-20_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	583					GRCh38	V40	AGFG1-BGHcLV25-20/Aligned.sortedByCoord.out.bam		ENCORE2	26268
AGFG1-BGHcLV25-20_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	583					GRCh38	V40	AGFG1-BGHcLV25-20/Aligned.sortedByCoord.out.bam		ENCORE2	26312
AGFG1-BGHcLV25-20_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	583					GRCh38	V40	AGFG1-BGHcLV25-20/Aligned.sortedByCoord.out.bam		ENCORE2	26356
AGFG1-BGHcLV25-20_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	583					GRCh38	V40	AGFG1-BGHcLV25-20/Aligned.sortedByCoord.out.bam		ENCORE2	26400