EIF3D RNA-Seq in K562

General Information


RBP	EIF3D
Cell_Line	K562
Method	shRNA
Exp_Name	EIF3D-BGKLV19-K562
ENCODE_series_ID	ENCSR940GDT
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR660ETT
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	EIF3D_BGKLV19_25B
Rep2	EIF3D_BGKLV19_26B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	91.3
Rep2_qPCR	88.2
Rep1_WB	83.5
Rep2_WB	83.2
Antibody Cat#	A301-758A
Antibody Lot#	A301-758A
Antibody DCC ID	ENCAB626JLZ
Status	Released
Project	ENCODE3
ID	472

Experiment Information (Status: Released)

	BGKLV19-25	BGKLV19-26
idx	232	233
TRCN#_or_BGC#	TRCN0000154123	TRCN0000154123
shRNA_or_gRNA_sequence	CGTAGTGATTGGGAAGTGAAA	CGTAGTGATTGGGAAGTGAAA
PAM
Name	EIF3D	EIF3D
Sample_ID	BGKLV19-25	BGKLV19-26
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	EIF3D	EIF3D
qPCR_result	91.3	88.2
Ave_qPCR	89.8
RT-qPCR_primer-F	aacggggaagtgtccttcat
RT-qPCR_primer-R	tcgctgagagtccagcttct
protein_conc	2438	2562
WB_result	83.5	83.2
Ave_WB	83.4
WB_DONE_date	12/5/2014
MW
IP	1	1
antibody_Cat#	A301-758A	A301-758A
Antibody DCC ID	ENCAB626JLZ	ENCAB626JLZ
submitted_to_DCC_date	4/2/2015
Rep1_TPM	187.498885	0
Rep2_TPM	261.741526	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	257	258

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3D	Product_ID: A301-758A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3D-human

Experiment Status

	BGKLV19-25	BGKLV19-26
Sample_ID	BGKLV19-25	BGKLV19-26
Sample Name	EIF3D_BGKLV19_25B	EIF3D_BGKLV19_26B
Sample Name	EIF3D_BGKLV19_25B	EIF3D_BGKLV19_26B
RBP	EIF3D	EIF3D
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	674	675

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-25	BGKLV19-26
Sample #
Sample Name	EIF3D-BGKLV19-25B	EIF3D-BGKLV19-26B
Sample_Name_Alias	EIF3D_BGKLV19_25B	EIF3D_BGKLV19_26B
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G8.png	DNA_Library_LV18-19/set1/H8.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/B1.png	RNA_Library_LV19-21-24/set1/D3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-25	BGKLV19-26
RBP	EIF3D	EIF3D
Batch_ID	BGKLV19	BGKLV19
WB_result	83.500	83.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2360	2361

Sequencing Information

	BGKLV19-25	BGKLV19-26
Sample_ID	BGKLV19-25	BGKLV19-26
Sample Name	EIF3D_BGKLV19_25B	EIF3D_BGKLV19_26B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	61,990,000	50,040,000
total_aligned_reads	57,870,468	46,357,628
unique_aligned_reads	52,771,862	42,417,246
percent_uniqueAligned	0.85130	0.84767
correlation_replicates	0.997003	0.997003
spikein_reads	296,374	373,324
percent_spikeins	0.00478	0.00746
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1002	1003

Data Submission Information

	BGKLV19-25	BGKLV19-25
ENCODE_alias	brenton-graveley:EIF3D_BGKLV19	brenton-graveley:EIF3D-BGKLV19-K562
ENCODE_accession	ENCSR660ETT	ENCSR940GDT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-25	BGKLV19-25
Sample Name	EIF3D_BGKLV19_25B	EIF3D_BGKLV19_25B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-05	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2886	6684

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
EIF3D_BGKLV19_25B_ATGTCA_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1002	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15114
EIF3D_BGKLV19_25B_ATGTCA_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1002	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15172
EIF3D_BGKLV19_25B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B_ATGTCA_L004_R1_001.fastq.gz,EIF3D_BGKLV19_25B_ATGTCA_L004_R2_001.fastq.gz		ENCORE2	15230
EIF3D_BGKLV19_25B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B/Aligned.sortedByCoord.out.bam		ENCORE2	15301
EIF3D_BGKLV19_25B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B/Aligned.sortedByCoord.out.bam		ENCORE2	15359
EIF3D_BGKLV19_25B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B/Aligned.sortedByCoord.out.bam		ENCORE2	15417
EIF3D_BGKLV19_25B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B/Aligned.sortedByCoord.out.bam		ENCORE2	15475
EIF3D_BGKLV19_25B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1002					GRCh38	V40	EIF3D_BGKLV19_25B_ATGTCA_L004_R1_001.fastq.gz,EIF3D_BGKLV19_25B_ATGTCA_L004_R2_001.fastq.gz		ENCORE2	16372
EIF3D_BGKLV19_26B_CCGTCC_L004_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1003	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15115
EIF3D_BGKLV19_26B_CCGTCC_L004_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1003	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15173
EIF3D_BGKLV19_26B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B_CCGTCC_L004_R1_001.fastq.gz,EIF3D_BGKLV19_26B_CCGTCC_L004_R2_001.fastq.gz		ENCORE2	15231
EIF3D_BGKLV19_26B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B/Aligned.sortedByCoord.out.bam		ENCORE2	15302
EIF3D_BGKLV19_26B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B/Aligned.sortedByCoord.out.bam		ENCORE2	15360
EIF3D_BGKLV19_26B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B/Aligned.sortedByCoord.out.bam		ENCORE2	15418
EIF3D_BGKLV19_26B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B/Aligned.sortedByCoord.out.bam		ENCORE2	15476
EIF3D_BGKLV19_26B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1003					GRCh38	V40	EIF3D_BGKLV19_26B_CCGTCC_L004_R1_001.fastq.gz,EIF3D_BGKLV19_26B_CCGTCC_L004_R2_001.fastq.gz		ENCORE2	16373