API5 RNA-Seq in K562

General Information


RBP	API5
Cell_Line	K562
Method	CRISPR
Exp_Name	API5-BGKcLV26-K562
ENCODE_series_ID	ENCSR958RMY
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR947EFJ
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	API5-BGKcLV26-27
Rep2	API5-BGKcLV26-28
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	59.3
Rep2_WB	50.0
Antibody Cat#	A302-784A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB023FOT
Status	Released
Project	ENCODE4
ID	792

Experiment Information (Status: Released)

	BGKcLV26-27	BGKcLV26-28
idx	884	885
TRCN#_or_BGC#	BGC#0000633	BGC#0000633
shRNA_or_gRNA_sequence	TCTCCAGGGTAAAACGGGTG	TCTCCAGGGTAAAACGGGTG
PAM	AGG	AGG
Name	API5_94	API5_94
Sample_ID	BGKcLV26-27	BGKcLV26-28
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	API5	API5
qPCR_result	38.0	48.8
Ave_qPCR	43.4
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4938	4823
WB_result	59.3	50.0
Ave_WB	54.7
WB_DONE_date	5/7/21	jess
MW	59kDa
IP	Rabbit / I
antibody_Cat#	A302-784A	LOT# 2
Antibody DCC ID	ENCAB023FOT
submitted_to_DCC_date
Rep1_TPM	98.9	0
Rep2_TPM	94.9	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5016	5017

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

	BGKcLV26-27	BGKcLV26-28
Sample_ID	BGKcLV26-27	BGKcLV26-28
Sample Name
Sample Name	API5-BGKcLV26-27	API5-BGKcLV26-28
RBP	API5	API5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9765	9766

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-27	BGKcLV26-28
Sample #	23	24
Sample Name	API5-BGKcLV26-27	API5-BGKcLV26-28
Sample_Name_Alias
Index Well Position	G03	H03
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	288	282
Peak_Molarity	108.00	65.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G3.png	DNA_Library_set48-49/set1/H3.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set48-49/set1/G3.png	RNA_Library_set48-49/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-27	BGKcLV26-28
RBP	API5	API5
Batch_ID	BGKcLV26	BGKcLV26
WB_result	59.300	50.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1582	1583

Sequencing Information

	BGKcLV26-27	BGKcLV26-28
Sample_ID	BGKcLV26-27	BGKcLV26-28
Sample Name	API5-BGKcLV26-27	API5-BGKcLV26-28
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	72,763,716	87,853,166
total_aligned_reads	63,834,874	73,230,804
unique_aligned_reads	58,550,752	66,968,590
percent_uniqueAligned	0.80467	0.76228
correlation_replicates	0.998668	0.998668
spikein_reads	27,110	25,914
percent_spikeins	0.00037	0.00029
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1759	1760

Data Submission Information

	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-28	BGKcLV26-28	BGKcLV26-28	BGKcLV26-28
ENCODE_alias	brenton-graveley:API5-BGKcLV26	brenton-graveley:API5-BGKcLV26-27	brenton-graveley:L-API5-BGKcLV26-27	brenton-graveley:API5-BGKcLV26-27_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGKcLV26-27_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGKcLV26-K562	brenton-graveley:API5-BGKcLV26-28	brenton-graveley:L-API5-BGKcLV26-28	brenton-graveley:API5-BGKcLV26-28_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:API5-BGKcLV26-28_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR947EFJ	ENCBS539IOW	ENCLB860ERZ	ENCFF043SVQ	ENCFF808TEX	ENCSR958RMY	ENCBS811YQF	ENCLB290DGA	ENCFF291XWS	ENCFF562OQX
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	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-27	BGKcLV26-28	BGKcLV26-28	BGKcLV26-28	BGKcLV26-28
Sample Name	API5-BGKcLV26-27	API5-BGKcLV26-27	API5-BGKcLV26-27	API5-BGKcLV26-27	API5-BGKcLV26-27	API5-BGKcLV26-27	API5-BGKcLV26-28	API5-BGKcLV26-28	API5-BGKcLV26-28	API5-BGKcLV26-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-19	2022-02-04	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2022-02-04	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		API5-BGKcLV26-27.pdf	L-API5-BGKcLV26-27.pdf				API5-BGKcLV26-28.pdf	L-API5-BGKcLV26-28.pdf
ID	3457	3548	3682	3816	3950	7089	3549	3683	3817	3951

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-BGKcLV26-27_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1759	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	3852
API5-BGKcLV26-27_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1759	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	3902
API5-BGKcLV26-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1759					GRCh38	V40	API5-BGKcLV26-27_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGKcLV26-27_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25539
API5-BGKcLV26-27_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1759					GRCh38	V40	API5-BGKcLV26-27_S29_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGKcLV26-27_S29_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25589
API5-BGKcLV26-27_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	1759					GRCh38	V40	API5-BGKcLV26-27/Aligned.sortedByCoord.out.bam		ENCORE2	26555
API5-BGKcLV26-27_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	1759					GRCh38	V40	API5-BGKcLV26-27/Aligned.sortedByCoord.out.bam		ENCORE2	26605
API5-BGKcLV26-27_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	1759					GRCh38	V40	API5-BGKcLV26-27/Aligned.sortedByCoord.out.bam		ENCORE2	26655
API5-BGKcLV26-27_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	1759					GRCh38	V40	API5-BGKcLV26-27/Aligned.sortedByCoord.out.bam		ENCORE2	26705
API5-BGKcLV26-28_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1760	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	3853
API5-BGKcLV26-28_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1760	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	3903
API5-BGKcLV26-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1760					GRCh38	V40	API5-BGKcLV26-28_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGKcLV26-28_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25540
API5-BGKcLV26-28_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1760					GRCh38	V40	API5-BGKcLV26-28_S30_L003_R1_001.filtered.trimmed.paired.fastq.gz,API5-BGKcLV26-28_S30_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25590
API5-BGKcLV26-28_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	1760					GRCh38	V40	API5-BGKcLV26-28/Aligned.sortedByCoord.out.bam		ENCORE2	26556
API5-BGKcLV26-28_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	1760					GRCh38	V40	API5-BGKcLV26-28/Aligned.sortedByCoord.out.bam		ENCORE2	26606
API5-BGKcLV26-28_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	1760					GRCh38	V40	API5-BGKcLV26-28/Aligned.sortedByCoord.out.bam		ENCORE2	26656
API5-BGKcLV26-28_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	1760					GRCh38	V40	API5-BGKcLV26-28/Aligned.sortedByCoord.out.bam		ENCORE2	26706