LIN28B RNA-Seq in K562

General Information


RBP	LIN28B
Cell_Line	K562
Method	shRNA
Exp_Name	LIN28B-BGKLV21-K562
ENCODE_series_ID	ENCSR812TGJ
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR598YQX
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	LIN28B_BGKLV21_27_17573
Rep2	LIN28B_BGKLV21_28_17574
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	86.5
Rep2_qPCR	68.7
Rep1_WB	79.9
Rep2_WB	79.4
Antibody Cat#	A303-588A
Antibody Lot#	A303-588A
Antibody DCC ID	ENCAB006PLV
Status	Released
Project	ENCODE3
ID	513

Experiment Information (Status: Released)

	BGKLV21-27	BGKLV21-27	BGKLV21-27	BGKLV21-28	BGKLV21-28	BGKLV21-28
idx	298	298	298	299	299	299
TRCN#_or_BGC#	TRCN0000144508	TRCN0000144508	TRCN0000144508	TRCN0000144508	TRCN0000144508	TRCN0000144508
shRNA_or_gRNA_sequence	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA	CCTGTTTAGGAAGTGAAAGAA
PAM
Name	LIN28B	LIN28B	LIN28B	LIN28B	LIN28B	LIN28B
Sample_ID	BGKLV21-27	BGKLV21-27	BGKLV21-27	BGKLV21-28	BGKLV21-28	BGKLV21-28
transduction_Date	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014	10/9/2014
days
RBP_name	LIN28B	LIN28B	LIN28B	LIN28B	LIN28B	LIN28B
qPCR_result	86.5	86.5	86.5	68.7	68.7	68.7
Ave_qPCR	77.6	77.6	77.6
RT-qPCR_primer-F	ggagcccctgtttaggaagt	ggagcccctgtttaggaagt	ggagcccctgtttaggaagt
RT-qPCR_primer-R	gcacttctttggctgaggag	gcacttctttggctgaggag	gcacttctttggctgaggag
protein_conc	2782	2782	2782	2964	2964	2964
WB_result	79.9	73.3	77.9	79.4	73.7	78.3
Ave_WB	79.6	73.5	78.1
WB_DONE_date	3/31/2015	4/18/2024	4/18/2024
MW		isoform 1	isoform 2
IP	1			1
antibody_Cat#	A303-588A	11965S	11965S	A303-588A	lot# 1	lot# 1
Antibody DCC ID	ENCAB006PLV			ENCAB006PLV
submitted_to_DCC_date	5/4/2015
Rep1_TPM	11.9171629	0	0	0	0	0
Rep2_TPM	6.37388528	0	0	0	0	0
Action
Library_start_date	5/19/2015			5/19/2015
repeat_library
Note
ID	329	331	333	330	332	334

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LIN28B	Product_ID: A303-588A Lot_ID: 1 Source: Bethyl Labs Target Name: LIN28B-human
LIN28B	Product_ID: 1965S Lot_ID: 1 Source: Cell Signaling Target Name: LIN28B-human

Experiment Status

	BGKLV21-27	BGKLV21-28
Sample_ID	BGKLV21-27	BGKLV21-28
Sample Name	LIN28B_BGKLV21_27_17573	LIN28B_BGKLV21_28_17574
Sample Name	LIN28B_BGKLV21_27_17573	LIN28B_BGKLV21_28_17574
RBP	LIN28B	LIN28B
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	758	759

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-27	BGKLV21-28
Sample #
Sample Name	LIN28B-BGKLV21-27	LIN28B-BGKLV21-28
Sample_Name_Alias	LIN28B_BGKLV21_27_17573	LIN28B_BGKLV21_28_17574
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A7.png	DNA_Library_LV21-24/set1/B7.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G9.png	RNA_Library_LV19-21-24/set1/H9.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-27	BGKLV21-28
RBP	LIN28B	LIN28B
Batch_ID	BGKLV21	BGKLV21
WB_result	79.900	79.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2444	2445

Sequencing Information

	BGKLV21-27	BGKLV21-28	BGKLV21-28
Sample_ID	BGKLV21-27	BGKLV21-28	BGKLV21-28
Sample Name	LIN28B_BGKLV21_27_17573	LIN28B_BGKLV21_28_17574	LIN28B_BGKLV21_28_17574
Pool ID	Pool-150615	Pool-150615	Pool-151215B
LocalServer_folder	set21	set21	set21
total_reads	43,210,000	21,070,000	41,979,706
total_aligned_reads	40,291,070	19,601,730	39,519,424
unique_aligned_reads	37,001,328	17,996,688	36,165,408
percent_uniqueAligned	0.85631	0.85414	0.86150
correlation_replicates	0.998368	0.998368
spikein_reads	198,320	107,896	209,068
percent_spikeins	0.00459	0.00512	0.00498
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	1050	1051	1379

Data Submission Information

	BGKLV21-27	BGKLV21-27
ENCODE_alias	brenton-graveley:LIN28B_BGKLV21	brenton-graveley:LIN28B-BGKLV21-K562
ENCODE_accession	ENCSR598YQX	ENCSR812TGJ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-27	BGKLV21-27
Sample Name	LIN28B_BGKLV21_27_17573	LIN28B_BGKLV21_27_17573
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2965	6800

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
LIN28B_BGKLV21_27_17573_GTCCGC_L002_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1050	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15938
LIN28B_BGKLV21_27_17573_GTCCGC_L002_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1050	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15982
LIN28B_BGKLV21_27_17573_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573_GTCCGC_L002_R1_001.fastq.gz,LIN28B_BGKLV21_27_17573_GTCCGC_L002_R2_001.fastq.gz		ENCORE2	16026
LIN28B_BGKLV21_27_17573_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573/Aligned.sortedByCoord.out.bam		ENCORE2	16070
LIN28B_BGKLV21_27_17573_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573/Aligned.sortedByCoord.out.bam		ENCORE2	16114
LIN28B_BGKLV21_27_17573_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573/Aligned.sortedByCoord.out.bam		ENCORE2	16158
LIN28B_BGKLV21_27_17573_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573/Aligned.sortedByCoord.out.bam		ENCORE2	16202
LIN28B_BGKLV21_27_17573_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1050					GRCh38	V40	LIN28B_BGKLV21_27_17573_GTCCGC_L002_R1_001.fastq.gz,LIN28B_BGKLV21_27_17573_GTCCGC_L002_R2_001.fastq.gz		ENCORE2	16246
LIN28B_BGKLV21_28_17574_GTGAAA_L002_R1_001.merged.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1051	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15939
LIN28B_BGKLV21_28_17574_GTGAAA_L002_R2_001.merged.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1051	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15983
LIN28B_BGKLV21_28_17574_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574_GTGAAA_L002_R1_001.merged.fastq.gz,LIN28B_BGKLV21_28_17574_GTGAAA_L002_R2_001.merged.fastq.gz		ENCORE2	16027
LIN28B_BGKLV21_28_17574_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574/Aligned.sortedByCoord.out.bam		ENCORE2	16071
LIN28B_BGKLV21_28_17574_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574/Aligned.sortedByCoord.out.bam		ENCORE2	16115
LIN28B_BGKLV21_28_17574_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574/Aligned.sortedByCoord.out.bam		ENCORE2	16159
LIN28B_BGKLV21_28_17574_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574/Aligned.sortedByCoord.out.bam		ENCORE2	16203
LIN28B_BGKLV21_28_17574_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1051					GRCh38	V40	LIN28B_BGKLV21_28_17574_GTGAAA_L002_R1_001.merged.fastq.gz,LIN28B_BGKLV21_28_17574_GTGAAA_L002_R2_001.merged.fastq.gz		ENCORE2	16247