FMR1 RNA-Seq in K562

General Information


RBP	FMR1
Cell_Line	K562
Method	shRNA
Exp_Name	FMR1-BGKLV36-K562
ENCODE_series_ID	ENCSR570ERU
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR555LCE
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	FMR1_BGKLV36-21
Rep2	FMR1_BGKLV36-22
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	56.2
Rep2_qPCR	52.6
Rep1_WB	85.6
Rep2_WB	76.9
Antibody Cat#	RN016P
Antibody Lot#	RN016P
Antibody DCC ID	ENCAB000BFK
Status	Released
Project	ENCODE3
ID	744

Experiment Information (Status: Released)

	BGKLV36-21	BGKLV36-22
idx	744	745
TRCN#_or_BGC#	TRCN0000059760	TRCN0000059760
shRNA_or_gRNA_sequence	CGAGATTTCATGAACAGTTTA	CGAGATTTCATGAACAGTTTA
PAM
Name	FMR1	FMR1
Sample_ID	BGKLV36-21	BGKLV36-22
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	FMR1	FMR1
qPCR_result	56.2	52.6
Ave_qPCR	54.4
RT-qPCR_primer-F	cgcggtcctggatatacttc
RT-qPCR_primer-R	tcctccttgtcctcttcctc
protein_conc	4100	3922
WB_result	85.6	76.9
Ave_WB	81.3
WB_DONE_date	6/23/16	WES
MW	71kDa
IP	1	1
antibody_Cat#	RN016P	RN016P
Antibody DCC ID	ENCAB000BFK	ENCAB000BFK
submitted_to_DCC_date	10/26/16
Rep1_TPM	9.8	0
Rep2_TPM	8.1	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	835	836

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FMR1	Product_ID: RN016P Lot_ID: 1 Source: MBLI Target Name: FMR1-human

Experiment Status

	BGKLV36-21	BGKLV36-22
Sample_ID	BGKLV36-21	BGKLV36-22
Sample Name	FMR1_BGKLV36-21	FMR1_BGKLV36-22
Sample Name	FMR1_BGKLV36-21	FMR1_BGKLV36-22
RBP	FMR1	FMR1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1281	1282

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-21	BGKLV36-22
Sample #
Sample Name	FMR1-BGKLV36-21	FMR1-BGKLV36-22
Sample_Name_Alias	FMR1_BGKLV36-21	FMR1_BGKLV36-22
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/G1.png	DNA_Library_LV36/set1/H1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/A5.png	RNA_Library_LV35_LV36/set1/B5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-21	BGKLV36-22
RBP	FMR1	FMR1
Batch_ID	BGKLV36	BGKLV36
WB_result	85.600	76.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2966	2967

Sequencing Information

	BGKLV36-21	BGKLV36-22
Sample_ID	BGKLV36-21	BGKLV36-22
Sample Name	FMR1_BGKLV36-21	FMR1_BGKLV36-22
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	86,428,922	79,168,414
total_aligned_reads	74,253,074	66,532,002
unique_aligned_reads	68,087,362	60,878,644
percent_uniqueAligned	0.78778	0.76898
correlation_replicates	0.988539	0.988539
spikein_reads	150,560	143,820
percent_spikeins	0.00174	0.00182
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1615	1616

Data Submission Information

	BGKLV36-21	BGKLV36-21
ENCODE_alias	brenton-graveley:FMR1_BGKLV36	brenton-graveley:FMR1-BGKLV36-K562
ENCODE_accession	ENCSR555LCE	ENCSR570ERU
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-21	BGKLV36-21
Sample Name	FMR1_BGKLV36-21	FMR1_BGKLV36-21
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3180	6716

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
FMR1_BGKLV36-21_ATGTCA_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1615	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21894
FMR1_BGKLV36-21_ATGTCA_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1615	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21912
FMR1_BGKLV36-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21_ATGTCA_L001_001.R1.fastq.gz,FMR1_BGKLV36-21_ATGTCA_L001_001.R2.fastq.gz		ENCORE2	21930
FMR1_BGKLV36-21_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21/Aligned.sortedByCoord.out.bam		ENCORE2	21948
FMR1_BGKLV36-21_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21/Aligned.sortedByCoord.out.bam		ENCORE2	21966
FMR1_BGKLV36-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21/Aligned.sortedByCoord.out.bam		ENCORE2	21984
FMR1_BGKLV36-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21/Aligned.sortedByCoord.out.bam		ENCORE2	22002
FMR1_BGKLV36-21_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1615					GRCh38	V40	FMR1_BGKLV36-21_ATGTCA_L001_001.R1.fastq.gz,FMR1_BGKLV36-21_ATGTCA_L001_001.R2.fastq.gz		ENCORE2	22020
FMR1_BGKLV36-22_CCGTCC_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1616	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21895
FMR1_BGKLV36-22_CCGTCC_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1616	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21913
FMR1_BGKLV36-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22_CCGTCC_L001_001.R1.fastq.gz,FMR1_BGKLV36-22_CCGTCC_L001_001.R2.fastq.gz		ENCORE2	21931
FMR1_BGKLV36-22_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22/Aligned.sortedByCoord.out.bam		ENCORE2	21949
FMR1_BGKLV36-22_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22/Aligned.sortedByCoord.out.bam		ENCORE2	21967
FMR1_BGKLV36-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22/Aligned.sortedByCoord.out.bam		ENCORE2	21985
FMR1_BGKLV36-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22/Aligned.sortedByCoord.out.bam		ENCORE2	22003
FMR1_BGKLV36-22_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1616					GRCh38	V40	FMR1_BGKLV36-22_CCGTCC_L001_001.R1.fastq.gz,FMR1_BGKLV36-22_CCGTCC_L001_001.R2.fastq.gz		ENCORE2	22021