AGFG1 RNA-Seq in K562

General Information


RBP	AGFG1
Cell_Line	K562
Method	CRISPR
Exp_Name	AGFG1-BGKcLV26-K562
ENCODE_series_ID	ENCSR348GXF
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR654SOD
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	AGFG1-BGKcLV26-15
Rep2	AGFG1-BGKcLV26-16
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR	12.2
Rep2_qPCR	2.7
Rep1_WB	70.6
Rep2_WB	66.5
Antibody Cat#	A301-792A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB794UUE
Status	Released
Project	ENCODE4
ID	786

Experiment Information (Status: Released)

	BGKcLV26-15	BGKcLV26-16
idx	868	869
TRCN#_or_BGC#	BGC#0000599	BGC#0000599
shRNA_or_gRNA_sequence	CCCCACCTACGTTAACATGA	CCCCACCTACGTTAACATGA
PAM	cgg	cgg
Name	AGFG1_94	AGFG1_94
Sample_ID	BGKcLV26-15	BGKcLV26-16
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	AGFG1	AGFG1
qPCR_result	12.2	2.7
Ave_qPCR	7.5
RT-qPCR_primer-F	tagtttggggctgaaaagga
RT-qPCR_primer-R	gctccagctcctcagtcaac
protein_conc	2000	2065
WB_result	70.6	66.5
Ave_WB	68.6
WB_DONE_date	5/21/21	jess
MW	58KD
IP	Rabbit / I
antibody_Cat#	A301-792A	LOT# 1
Antibody DCC ID	ENCAB794UUE	10/22/21
submitted_to_DCC_date
Rep1_TPM	25.8	0
Rep2_TPM	24.4	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5000	5001

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

	BGKcLV26-15	BGKcLV26-16
Sample_ID	BGKcLV26-15	BGKcLV26-16
Sample Name
Sample Name	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-16
RBP	AGFG1	AGFG1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9753	9754

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-15	BGKcLV26-16
Sample #	11	12
Sample Name	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-16
Sample_Name_Alias
Index Well Position	C02	D02
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	318	286
Peak_Molarity	90.80	65.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/C2.png	DNA_Library_set48-49/set1/D2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set48-49/set1/C2.png	RNA_Library_set48-49/set1/D2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-15	BGKcLV26-16
RBP	AGFG1	AGFG1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	70.600	66.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1570	1571

Sequencing Information

	BGKcLV26-15	BGKcLV26-16
Sample_ID	BGKcLV26-15	BGKcLV26-16
Sample Name	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-16
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	61,045,566	63,499,198
total_aligned_reads	49,759,622	56,234,324
unique_aligned_reads	45,282,636	51,194,396
percent_uniqueAligned	0.74178	0.80622
correlation_replicates	0.999067	0.999067
spikein_reads	27,004	18,432
percent_spikeins	0.00044	0.00029
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1747	1748

Data Submission Information

	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-16	BGKcLV26-16	BGKcLV26-16	BGKcLV26-16
ENCODE_alias	brenton-graveley:AGFG1-BGKcLV26	brenton-graveley:AGFG1-BGKcLV26-15	brenton-graveley:L-AGFG1-BGKcLV26-15	brenton-graveley:AGFG1-BGKcLV26-15_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGKcLV26-15_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGKcLV26-K562	brenton-graveley:AGFG1-BGKcLV26-16	brenton-graveley:L-AGFG1-BGKcLV26-16	brenton-graveley:AGFG1-BGKcLV26-16_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:AGFG1-BGKcLV26-16_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR654SOD	ENCBS035SQW	ENCLB274FLM	ENCFF689RZI	ENCFF249BQE	ENCSR348GXF	ENCBS063IQR	ENCLB927MKA	ENCFF196VIH	ENCFF329NNW
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	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-15	BGKcLV26-16	BGKcLV26-16	BGKcLV26-16	BGKcLV26-16
Sample Name	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-15	AGFG1-BGKcLV26-16	AGFG1-BGKcLV26-16	AGFG1-BGKcLV26-16	AGFG1-BGKcLV26-16
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		AGFG1-BGKcLV26-15.pdf	L-AGFG1-BGKcLV26-15.pdf				AGFG1-BGKcLV26-16.pdf	L-AGFG1-BGKcLV26-16.pdf
ID	3451	3536	3670	3804	3938	7073	3537	3671	3805	3939

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-BGKcLV26-15_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1747	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	3840
AGFG1-BGKcLV26-15_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1747	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	3890
AGFG1-BGKcLV26-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1747					GRCh38	V40	AGFG1-BGKcLV26-15_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGKcLV26-15_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25527
AGFG1-BGKcLV26-15_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1747					GRCh38	V40	AGFG1-BGKcLV26-15_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGKcLV26-15_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25577
AGFG1-BGKcLV26-15_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	1747					GRCh38	V40	AGFG1-BGKcLV26-15/Aligned.sortedByCoord.out.bam		ENCORE2	26543
AGFG1-BGKcLV26-15_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	1747					GRCh38	V40	AGFG1-BGKcLV26-15/Aligned.sortedByCoord.out.bam		ENCORE2	26593
AGFG1-BGKcLV26-15_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	1747					GRCh38	V40	AGFG1-BGKcLV26-15/Aligned.sortedByCoord.out.bam		ENCORE2	26643
AGFG1-BGKcLV26-15_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	1747					GRCh38	V40	AGFG1-BGKcLV26-15/Aligned.sortedByCoord.out.bam		ENCORE2	26693
AGFG1-BGKcLV26-16_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1748	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	3841
AGFG1-BGKcLV26-16_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1748	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	3891
AGFG1-BGKcLV26-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1748					GRCh38	V40	AGFG1-BGKcLV26-16_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGKcLV26-16_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25528
AGFG1-BGKcLV26-16_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1748					GRCh38	V40	AGFG1-BGKcLV26-16_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz,AGFG1-BGKcLV26-16_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25578
AGFG1-BGKcLV26-16_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	1748					GRCh38	V40	AGFG1-BGKcLV26-16/Aligned.sortedByCoord.out.bam		ENCORE2	26544
AGFG1-BGKcLV26-16_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	1748					GRCh38	V40	AGFG1-BGKcLV26-16/Aligned.sortedByCoord.out.bam		ENCORE2	26594
AGFG1-BGKcLV26-16_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	1748					GRCh38	V40	AGFG1-BGKcLV26-16/Aligned.sortedByCoord.out.bam		ENCORE2	26644
AGFG1-BGKcLV26-16_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	1748					GRCh38	V40	AGFG1-BGKcLV26-16/Aligned.sortedByCoord.out.bam		ENCORE2	26694