NFX1 RNA-Seq in K562

General Information


RBP	NFX1
Cell_Line	K562
Method	shRNA
Exp_Name	NFX1-BGKLV13-K562
ENCODE_series_ID	ENCSR440WRA
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR007XKL
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	NFX1_BGKLV13_25
Rep2	NFX1_BGKLV13_26
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	52.0
Rep2_qPCR	45.7
Rep1_WB
Rep2_WB
Antibody Cat#	A302-914A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB841CSS
Status	Released
Project	ENCODE3
ID	368

Experiment Information (Status: Released)

	BGKLV13-25	BGKLV13-26
idx	158	159
TRCN#_or_BGC#	TRCN0000014906	TRCN0000014906
shRNA_or_gRNA_sequence	GCAGAGAAGATACCCACAGAA	GCAGAGAAGATACCCACAGAA
PAM
Name	NFX1	NFX1
Sample_ID	BGKLV13-25	BGKLV13-26
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	NFX1	NFX1
qPCR_result	52.0	45.7
Ave_qPCR	48.9
RT-qPCR_primer-F	agaatgtggaaacgcacaca
RT-qPCR_primer-R	cgtgacacgaaccaattcac
protein_conc	2120	1987
WB_result
Ave_WB
WB_DONE_date
MW	124kDa
IP	1	1
antibody_Cat#	A302-914A	A302-914A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	14.5634679	0
Rep2_TPM	10.6196596	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	173	174

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV13-25	BGKLV13-26
Sample_ID	BGKLV13-25	BGKLV13-26
Sample Name	NFX1_BGKLV13_25	NFX1_BGKLV13_26
Sample Name	NFX1_BGKLV13_25	NFX1_BGKLV13_26
RBP	NFX1	NFX1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	458	459

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-25	BGKLV13-26
Sample #
Sample Name	NFX1-BGKLV13-25	NFX1-BGKLV13-26
Sample_Name_Alias	NFX1_BGKLV13_25	NFX1_BGKLV13_26
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D3.png	DNA_Library_LV13-14/set1/E3.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G11.png	RNA_Library_LV12/set1/H11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-25	BGKLV13-26
RBP	NFX1	NFX1
Batch_ID	BGKLV13	BGKLV13
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2138	2139

Sequencing Information

	BGKLV13-25	BGKLV13-26
Sample_ID	BGKLV13-25	BGKLV13-26
Sample Name	NFX1_BGKLV13_25	NFX1_BGKLV13_26
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	45,070,000	48,330,000
total_aligned_reads	41,566,390	44,053,924
unique_aligned_reads	38,358,364	40,607,950
percent_uniqueAligned	0.85108	0.84022
correlation_replicates	0.996243	0.996243
spikein_reads	191,566	190,790
percent_spikeins	0.00425	0.00395
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	780	781

Data Submission Information

	BGKLV13-25	BGKLV13-25
ENCODE_alias	brenton-graveley:NFX1_BGKLV13	brenton-graveley:NFX1-BGKLV13-K562
ENCODE_accession	ENCSR007XKL	ENCSR440WRA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-25	BGKLV13-25
Sample Name	NFX1_BGKLV13_25	NFX1_BGKLV13_25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2778	6822

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
NFX1_BGKLV13_25_GTGGCC_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	780	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13386
NFX1_BGKLV13_25_GTGGCC_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	780	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13438
NFX1_BGKLV13_25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25_GTGGCC_L003_R1_001.fastq.gz,NFX1_BGKLV13_25_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	13490
NFX1_BGKLV13_25_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25/Aligned.sortedByCoord.out.bam		ENCORE2	13542
NFX1_BGKLV13_25_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25/Aligned.sortedByCoord.out.bam		ENCORE2	13594
NFX1_BGKLV13_25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25/Aligned.sortedByCoord.out.bam		ENCORE2	13646
NFX1_BGKLV13_25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25/Aligned.sortedByCoord.out.bam		ENCORE2	13698
NFX1_BGKLV13_25_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	780					GRCh38	V40	NFX1_BGKLV13_25_GTGGCC_L003_R1_001.fastq.gz,NFX1_BGKLV13_25_GTGGCC_L003_R2_001.fastq.gz		ENCORE2	13750
NFX1_BGKLV13_26_GTTTCG_L003_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	781	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13387
NFX1_BGKLV13_26_GTTTCG_L003_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	781	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13439
NFX1_BGKLV13_26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26_GTTTCG_L003_R1_001.fastq.gz,NFX1_BGKLV13_26_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	13491
NFX1_BGKLV13_26_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26/Aligned.sortedByCoord.out.bam		ENCORE2	13543
NFX1_BGKLV13_26_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26/Aligned.sortedByCoord.out.bam		ENCORE2	13595
NFX1_BGKLV13_26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26/Aligned.sortedByCoord.out.bam		ENCORE2	13647
NFX1_BGKLV13_26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26/Aligned.sortedByCoord.out.bam		ENCORE2	13699
NFX1_BGKLV13_26_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	781					GRCh38	V40	NFX1_BGKLV13_26_GTTTCG_L003_R1_001.fastq.gz,NFX1_BGKLV13_26_GTTTCG_L003_R2_001.fastq.gz		ENCORE2	13751