EIF2B3 RNA-Seq in K562

General Information


RBP	EIF2B3
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF2B3-BGKcLV15-K562
ENCODE_series_ID	ENCSR513MXV
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR786OLN
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	EIF2B3-BGKcLV15-27
Rep2	EIF2B3-BGKcLV15-28
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	53.3
Rep2_qPCR	56.1
Rep1_WB	83.7
Rep2_WB	86.9
Antibody Cat#	MA1-078
Antibody Lot#	LOT# NL176595
Antibody DCC ID	ENCAB985GAJ
Status	Released
Project	ENCODE4
ID	125

Experiment Information (Status: Released)

	BGKcLV15-27	BGKcLV15-28
idx	563	564
TRCN#_or_BGC#	BGC#0000388	BGC#0000388
shRNA_or_gRNA_sequence	AACAGACGTTGCCTTACATG	AACAGACGTTGCCTTACATG
PAM	AGG	AGG
Name	EIF2B gamma_89	EIF2B gamma_89
Sample_ID	BGKcLV15-27	BGKcLV15-28
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	EIF2B3	EIF2B3
qPCR_result	53.3	56.1
Ave_qPCR	54.7
RT-qPCR_primer-F	tggtacccattgaacctgct
RT-qPCR_primer-R	ccttttgaacatccctggtt
protein_conc	5663	5795
WB_result	83.7	86.9
Ave_WB	85.3
WB_DONE_date	4/21/19
MW	58KD
IP	Mouse / Ig
antibody_Cat#	MA1-078	LOT# NL176595
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	100.6	0
Rep2_TPM	34.1	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4673	4674

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2B3	Product_ID: MA1-078 Lot_ID: NL176595 Source: Thermo Fisher Target Name: EIF2B3-human

Experiment Status

	BGKcLV15-27	BGKcLV15-28
Sample_ID	BGKcLV15-27	BGKcLV15-28
Sample Name
Sample Name	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-28
RBP	EIF2B3	EIF2B3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5339	5340

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-27	BGKcLV15-28
Sample #	9	10
Sample Name	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-28
Sample_Name_Alias
Index Well Position	A02	B02
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-A2	1-B2
Tecan	43.04	39.51
Tecan_date	2019-12-10	2019-12-10
Size_bp	267	267
Peak_Molarity	23.50	19.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/A2.png	DNA_Library_set43-44/set1/B2.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/A2.png	RNA_Library_set43-44/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-27	BGKcLV15-28
RBP	EIF2B3	EIF2B3
Batch_ID	BGKcLV15	BGKcLV15
WB_result	83.700	86.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	585	586

Sequencing Information

	BGKcLV15-27	BGKcLV15-28
Sample_ID	BGKcLV15-27	BGKcLV15-28
Sample Name	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-28
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	94,494,840	165,679,646
total_aligned_reads	88,486,840	124,469,006
unique_aligned_reads	80,766,562	113,295,000
percent_uniqueAligned	0.85472	0.68382
correlation_replicates	0.995053	0.995053
spikein_reads	66,210	56,450
percent_spikeins	0.00070	0.00034
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	91	92

Data Submission Information

	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-28	BGKcLV15-28	BGKcLV15-28	BGKcLV15-28
ENCODE_alias	brenton-graveley:EIF2B3-BGKcLV15	brenton-graveley:EIF2B3-BGKcLV15-27	brenton-graveley:L-EIF2B3-BGKcLV15-27	brenton-graveley:EIF2B3-BGKcLV15-27_S9_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGKcLV15-27_S9_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGKcLV15-K562	brenton-graveley:EIF2B3-BGKcLV15-28	brenton-graveley:L-EIF2B3-BGKcLV15-28	brenton-graveley:EIF2B3-BGKcLV15-28_S10_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGKcLV15-28_S10_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR786OLN	ENCBS422SUU	ENCLB532NOM	ENCFF812KUN	ENCFF808GPR	ENCSR513MXV	ENCBS726XNC	ENCLB505VFF	ENCFF900UHQ	ENCFF248OUM
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	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-27	BGKcLV15-28	BGKcLV15-28	BGKcLV15-28	BGKcLV15-28
Sample Name	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-27	EIF2B3-BGKcLV15-28	EIF2B3-BGKcLV15-28	EIF2B3-BGKcLV15-28	EIF2B3-BGKcLV15-28
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		EIF2B3-BGKcLV15-27.pdf	L-EIF2B3-BGKcLV15-27.pdf				EIF2B3-BGKcLV15-28.pdf	L-EIF2B3-BGKcLV15-28.pdf
ID	21	124	288	486	538	7199	125	289	487	539

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
EIF2B3-BGKcLV15-27_S9_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	91	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	83
EIF2B3-BGKcLV15-27_S9_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	91	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	135
EIF2B3-BGKcLV15-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	91					GRCh38	V40	EIF2B3-BGKcLV15-27_S9_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGKcLV15-27_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24374
EIF2B3-BGKcLV15-27_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	91					GRCh38	V40	EIF2B3-BGKcLV15-27/Aligned.sortedByCoord.out.bam		ENCORE2	24426
EIF2B3-BGKcLV15-27_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	91					GRCh38	V40	EIF2B3-BGKcLV15-27/Aligned.sortedByCoord.out.bam		ENCORE2	24478
EIF2B3-BGKcLV15-27_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	91					GRCh38	V40	EIF2B3-BGKcLV15-27/Aligned.sortedByCoord.out.bam		ENCORE2	24530
EIF2B3-BGKcLV15-27_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	91					GRCh38	V40	EIF2B3-BGKcLV15-27/Aligned.sortedByCoord.out.bam		ENCORE2	24582
EIF2B3-BGKcLV15-27_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	91					GRCh38	V40	EIF2B3-BGKcLV15-27_S9_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGKcLV15-27_S9_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24634
EIF2B3-BGKcLV15-28_S10_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	92	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	84
EIF2B3-BGKcLV15-28_S10_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	92	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	136
EIF2B3-BGKcLV15-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	92					GRCh38	V40	EIF2B3-BGKcLV15-28_S10_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGKcLV15-28_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24375
EIF2B3-BGKcLV15-28_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	92					GRCh38	V40	EIF2B3-BGKcLV15-28/Aligned.sortedByCoord.out.bam		ENCORE2	24427
EIF2B3-BGKcLV15-28_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	92					GRCh38	V40	EIF2B3-BGKcLV15-28/Aligned.sortedByCoord.out.bam		ENCORE2	24479
EIF2B3-BGKcLV15-28_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	92					GRCh38	V40	EIF2B3-BGKcLV15-28/Aligned.sortedByCoord.out.bam		ENCORE2	24531
EIF2B3-BGKcLV15-28_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	92					GRCh38	V40	EIF2B3-BGKcLV15-28/Aligned.sortedByCoord.out.bam		ENCORE2	24583
EIF2B3-BGKcLV15-28_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	92					GRCh38	V40	EIF2B3-BGKcLV15-28_S10_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGKcLV15-28_S10_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24635