EIF3H RNA-Seq in K562

General Information


RBP	EIF3H
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3H-BGKcLV04-K562
ENCODE_series_ID	ENCSR705ZCB
Batch_ID	BGKcLV04
Pool ID	Pool-161129
Local_Set_Name	BGKcLV04
ENCODE_KD_Exp_ID	ENCSR096WVE
ENCODE_CN_Exp_ID	ENCSR226KWO
Rep1	EIF3H_BGKcLV04_11B
Rep2	EIF3H_BGKcLV04_12B
CN1	NT_BGKcLV04-1B
CN2	NT_BGKcLV04-2B
Rep1_qPCR	73.2
Rep2_qPCR	85.7
Rep1_WB	69.1
Rep2_WB	73.6
Antibody Cat#	A301-754A
Antibody Lot#	A301-754A
Antibody DCC ID	ENCAB957ITF
Status	Released
Project	ENCODE3
ID	591

Experiment Information (Status: Released)

	BGKcLV04-11	BGKcLV04-12
idx	59	60
TRCN#_or_BGC#	BGC#0000033	BGC#0000033
shRNA_or_gRNA_sequence	TGGGTCTGGTTGTAGAAGAT	TGGGTCTGGTTGTAGAAGAT
PAM
Name	EIF3H_2	EIF3H_2
Sample_ID	BGKcLV04-11	BGKcLV04-12
transduction_Date	6/22/16	6/22/16
days	day 6	day 6
RBP_name	EIF3H	EIF3H
qPCR_result	73.2	85.7
Ave_qPCR	79.4
RT-qPCR_primer-F	gcacacagaggatgatgctg
RT-qPCR_primer-R	ataccagcccacgtgaagat
protein_conc	2356	2232
WB_result	69.1	73.6
Ave_WB	71.4
WB_DONE_date	7/7/16
MW	40
IP	1
antibody_Cat#	A301-754A	A301-754A
Antibody DCC ID	ENCAB957ITF	ENCAB957ITF
submitted_to_DCC_date	10/26/16
Rep1_TPM	126.2	0
Rep2_TPM	193.1	0
Action	Ready	Ready
Library_start_date	08/15/16	08/15/16
repeat_library
Note
ID	4157	4158

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3H	Product_ID: A301-754A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3H-human

Experiment Status

	BGKcLV04-11	BGKcLV04-12
Sample_ID	BGKcLV04-11	BGKcLV04-12
Sample Name	EIF3H_BGKcLV04_11B	EIF3H_BGKcLV04_12B
Sample Name	EIF3H_BGKcLV04_11B	EIF3H_BGKcLV04_12B
RBP	EIF3H	EIF3H
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1315	1316

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV04-11	BGKcLV04-12
Sample #
Sample Name	EIF3H-BGKcLV04-11B	EIF3H-BGKcLV04-12B
Sample_Name_Alias	EIF3H_BGKcLV04_11B	EIF3H_BGKcLV04_12B
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-07	2016-11-07
Lib_ID	Lib-161107	Lib-161107
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/E2.png	DNA_Library_cLV04/set1/F1.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV37_38/set3/A1.png	RNA_Library_LV37_38/set3/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV04-11	BGKcLV04-12
RBP	EIF3H	EIF3H
Batch_ID	BGKcLV04	BGKcLV04
WB_result	69.100	73.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3024	3025

Sequencing Information

	BGKcLV04-11	BGKcLV04-12
Sample_ID	BGKcLV04-11	BGKcLV04-12
Sample Name	EIF3H_BGKcLV04_11B	EIF3H_BGKcLV04_12B
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	BGKcLV04	BGKcLV04
total_reads	45,229,132	64,416,212
total_aligned_reads	39,972,194	57,237,284
unique_aligned_reads	36,514,146	52,074,576
percent_uniqueAligned	0.80731	0.80841
correlation_replicates	0.998707	0.998707
spikein_reads	173,902	274,972
percent_spikeins	0.00384	0.00427
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1661	1662

Data Submission Information

	BGKcLV04-11	BGKcLV04-11
ENCODE_alias	brenton-graveley:EIF3H_BGKcLV04	brenton-graveley:EIF3H-BGKcLV04-K562
ENCODE_accession	ENCSR096WVE	ENCSR705ZCB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV04-11	BGKcLV04-11
Sample Name	EIF3H_BGKcLV04_11B	EIF3H_BGKcLV04_11B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-12-12	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3197	6688

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
EIF3H_BGKcLV04_11B_CAGATC_L005_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1661	HiSeq2500	100	paired-ended	1				NT_BGKcLV04-1B_TTAGGC_L004_001.R1.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R1.fastq.gz	ENCODE3	23054
EIF3H_BGKcLV04_11B_CAGATC_L005_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1661	HiSeq2500	100	paired-ended	2				NT_BGKcLV04-1B_TTAGGC_L004_001.R2.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R2.fastq.gz	ENCODE3	23064
EIF3H_BGKcLV04_11B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B_CAGATC_L005_001.R1.fastq.gz,EIF3H_BGKcLV04_11B_CAGATC_L005_001.R2.fastq.gz		ENCORE2	23074
EIF3H_BGKcLV04_11B_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B/Aligned.sortedByCoord.out.bam		ENCORE2	23084
EIF3H_BGKcLV04_11B_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B/Aligned.sortedByCoord.out.bam		ENCORE2	23094
EIF3H_BGKcLV04_11B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B/Aligned.sortedByCoord.out.bam		ENCORE2	23104
EIF3H_BGKcLV04_11B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B/Aligned.sortedByCoord.out.bam		ENCORE2	23114
EIF3H_BGKcLV04_11B_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1661					GRCh38	V40	EIF3H_BGKcLV04_11B_CAGATC_L005_001.R1.fastq.gz,EIF3H_BGKcLV04_11B_CAGATC_L005_001.R2.fastq.gz		ENCORE2	23124
EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1662	HiSeq2500	100	paired-ended	1				NT_BGKcLV04-1B_TTAGGC_L004_001.R1.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R1.fastq.gz	ENCODE3	23055
EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1662	HiSeq2500	100	paired-ended	2				NT_BGKcLV04-1B_TTAGGC_L004_001.R2.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R2.fastq.gz	ENCODE3	23065
EIF3H_BGKcLV04_12B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R1.fastq.gz,EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R2.fastq.gz		ENCORE2	23075
EIF3H_BGKcLV04_12B_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B/Aligned.sortedByCoord.out.bam		ENCORE2	23085
EIF3H_BGKcLV04_12B_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B/Aligned.sortedByCoord.out.bam		ENCORE2	23095
EIF3H_BGKcLV04_12B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B/Aligned.sortedByCoord.out.bam		ENCORE2	23105
EIF3H_BGKcLV04_12B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B/Aligned.sortedByCoord.out.bam		ENCORE2	23115
EIF3H_BGKcLV04_12B_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1662					GRCh38	V40	EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R1.fastq.gz,EIF3H_BGKcLV04_12B_ACTTGA_L005_001.R2.fastq.gz		ENCORE2	23125