EIF2AK1 RNA-Seq in K562

General Information


RBP	EIF2AK1
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2AK1-BGKcLV15-K562
ENCODE_series_ID	ENCSR340GYM
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR667WZB
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	EIF2AK1-BGKcLV15-23
Rep2	EIF2AK1-BGKcLV15-24
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	77.2
Rep2_qPCR	74.6
Rep1_WB	79.0
Rep2_WB	75.2
Antibody Cat#	PA5-29409
Antibody Lot#	LOT# TK267536A
Antibody DCC ID	ENCAB472KCD
Status	Released
Project	ENCODE4
ID	124

Experiment Information (Status: Released)

	BGKcLV15-23	BGKcLV15-23	BGKcLV15-24	BGKcLV15-24
idx	555	559	556	560
TRCN#_or_BGC#	BGC#0000345	BGC#0000345	BGC#0000345	BGC#0000345
shRNA_or_gRNA_sequence	TTGTTGGCTATCACACCGCG	TTGTTGGCTATCACACCGCG	TTGTTGGCTATCACACCGCG	TTGTTGGCTATCACACCGCG
PAM	tgg	tgg	tgg	tgg
Name	EIF2AK1-97	EIF2AK1-97	EIF2AK1-97	EIF2AK1-97
Sample_ID	BGKcLV15-23	BGKcLV15-23	BGKcLV15-24	BGKcLV15-24
transduction_Date	4/2/19	4/2/19	4/2/19	4/2/19
days	Day 6	Day 6	Day 6	Day 6
RBP_name	EIF2AK1	EIF2AK1	EIF2AK1	EIF2AK1
qPCR_result	77.2		74.6
Ave_qPCR	75.9
RT-qPCR_primer-F	TTGCCATCTCTGGAAGTGCT
RT-qPCR_primer-R	CGTTTTTCTTTTTCTGGGGTG
protein_conc	6031	6031	5665	5665
WB_result	79.0	NO CLEAR BAND	75.2
Ave_WB	77.1
WB_DONE_date	4/10/19,4/11/19,4/30	4/10/19,4/11/19,4/30	WES, LICOR	WES, LICOR
MW	71KD	71KD
IP	Rabbit / I	Rabbit / I
antibody_Cat#	PA5-29409	711581	LOT# TK267536A
Antibody DCC ID	ENCAB472KCD
submitted_to_DCC_date	4/17/19
Rep1_TPM	94.1	94.1	0	0
Rep2_TPM	102.6	102.6	0	0
Action	Ready		Ready
Library_start_date	05/30/19		05/30/19
repeat_library
Note
ID	4665	4669	4666	4670

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2AK1	Product_ID: PA5-29409 Lot_ID: TK267536A Source: Thermo Fisher Target Name: EIF2AK1-human

Experiment Status

	BGKcLV15-23	BGKcLV15-24
Sample_ID	BGKcLV15-23	BGKcLV15-24
Sample Name
Sample Name	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-24
RBP	EIF2AK1	EIF2AK1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5337	5338

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-23	BGKcLV15-24
Sample #	7	8
Sample Name	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-24
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-G1	1-H1
Tecan	33.46	27.99
Tecan_date	2019-12-10	2019-12-10
Size_bp	262	271
Peak_Molarity	16.80	11.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G1.png	DNA_Library_set43-44/set1/H1.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set43-44/set1/G1.png	RNA_Library_set43-44/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-23	BGKcLV15-24
RBP	EIF2AK1	EIF2AK1
Batch_ID	BGKcLV15	BGKcLV15
WB_result	79.000	75.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	583	584

Sequencing Information

	BGKcLV15-23	BGKcLV15-24
Sample_ID	BGKcLV15-23	BGKcLV15-24
Sample Name	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-24
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	175,413,446	100,781,264
total_aligned_reads	148,073,656	95,277,774
unique_aligned_reads	134,229,082	86,873,658
percent_uniqueAligned	0.76522	0.86200
correlation_replicates	0.992243	0.992243
spikein_reads	78,908	64,298
percent_spikeins	0.00045	0.00064
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	89	90

Data Submission Information

	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-24	BGKcLV15-24	BGKcLV15-24	BGKcLV15-24
ENCODE_alias	brenton-graveley:EIF2AK1-BGKcLV15	brenton-graveley:EIF2AK1-BGKcLV15-23	brenton-graveley:L-EIF2AK1-BGKcLV15-23	brenton-graveley:EIF2AK1-BGKcLV15-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2AK1-BGKcLV15-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2AK1-BGKcLV15-K562	brenton-graveley:EIF2AK1-BGKcLV15-24	brenton-graveley:L-EIF2AK1-BGKcLV15-24	brenton-graveley:EIF2AK1-BGKcLV15-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2AK1-BGKcLV15-24_S8_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR667WZB	ENCBS902FGA	ENCLB946ISK	ENCFF994HUD	ENCFF870YWT	ENCSR340GYM	ENCBS403NOH	ENCLB294ORG	ENCFF636KYE	ENCFF031NSR
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	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-23	BGKcLV15-24	BGKcLV15-24	BGKcLV15-24	BGKcLV15-24
Sample Name	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-23	EIF2AK1-BGKcLV15-24	EIF2AK1-BGKcLV15-24	EIF2AK1-BGKcLV15-24	EIF2AK1-BGKcLV15-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		EIF2AK1-BGKcLV15-23.pdf	L-EIF2AK1-BGKcLV15-23.pdf				EIF2AK1-BGKcLV15-24.pdf	L-EIF2AK1-BGKcLV15-24.pdf
ID	20	122	286	484	536	7196	123	287	485	537

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
EIF2AK1-BGKcLV15-23_S7_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	89	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	81
EIF2AK1-BGKcLV15-23_S7_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	89	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	133
EIF2AK1-BGKcLV15-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK1-BGKcLV15-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24372
EIF2AK1-BGKcLV15-23_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23/Aligned.sortedByCoord.out.bam		ENCORE2	24424
EIF2AK1-BGKcLV15-23_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23/Aligned.sortedByCoord.out.bam		ENCORE2	24476
EIF2AK1-BGKcLV15-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23/Aligned.sortedByCoord.out.bam		ENCORE2	24528
EIF2AK1-BGKcLV15-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23/Aligned.sortedByCoord.out.bam		ENCORE2	24580
EIF2AK1-BGKcLV15-23_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	89					GRCh38	V40	EIF2AK1-BGKcLV15-23_S7_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK1-BGKcLV15-23_S7_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24632
EIF2AK1-BGKcLV15-24_S8_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	90	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	82
EIF2AK1-BGKcLV15-24_S8_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	90	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	134
EIF2AK1-BGKcLV15-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK1-BGKcLV15-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24373
EIF2AK1-BGKcLV15-24_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24/Aligned.sortedByCoord.out.bam		ENCORE2	24425
EIF2AK1-BGKcLV15-24_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24/Aligned.sortedByCoord.out.bam		ENCORE2	24477
EIF2AK1-BGKcLV15-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24/Aligned.sortedByCoord.out.bam		ENCORE2	24529
EIF2AK1-BGKcLV15-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24/Aligned.sortedByCoord.out.bam		ENCORE2	24581
EIF2AK1-BGKcLV15-24_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	90					GRCh38	V40	EIF2AK1-BGKcLV15-24_S8_R1_001.filtered.trimmed.paired.fastq.gz,EIF2AK1-BGKcLV15-24_S8_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24633