title: Batch 2_time point 6_2

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

data_processing:
Iso-Seq analysis was performed on the SMRT portal website. Reads from different replicates and time points were processed independently. Standard parameters were used to cluster and polish reads in the Iso-Seq protocol.
Isoseq reads were aligned to the v2.29 Sch.pombe genome using GMAP
Isoforms were detected using SpliceHunter (https://bitbucket.org/canzar/splicehunter)
Genome_build: v2.29 Sch.pombe genome
Supplementary_files_format_and_content: tab deliminated file containing the coordinates of isoforms, numbers of CCS full length reads,  types and locations of alternative splicing

organism: Schizosaccharomyces pombe

source_name: fission yeast meiotic cells

growth_protocol: SP2910 (mat1-PΔ17/mat1-M-smt-o his2/+ leu1-32/+ ura4/+ ade6-M210/ade6-M216) was grown in 1ml YES medium overnight and diluted in EMM culture at an OD of 0.1. Cells were harvested and washed when they entered into the log phase (~OD 0.6) and resuspended in EMM without NH4Cl (EMM-N). 10 OD of cells were collected from 0 to 10 hours after resuspending in EMM-N medium every 2 hours

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (Qiagen, 74106) and polyA selection was performed using the Poly(A)Purist MAG kit (Invitrogen AM1922).
cDNA libraries were synthesized using the SMARTer PCR cDNA synthesis kit (Clontech, 634926). SMRT libraries were generated in the Johns Hopkins Deep Sequencing and Microarray core facility using the Pacific Biosciences’s template prep kit.

tag: replicate

tag: time point

value: meiosis hour 10


title: Batch 2_time point 2_2

status: Public on Nov 10 2016

type: SRA

city: Pittsburgh

state: PA

country: USA

library_source: transcriptomic

molecule: total RNA

value: meiosis hour 2


title: Batch 2_time point 1_2

value: meiosis hour 0


title: Batch 2_time point 6_1


title: Batch 2_time point 3_2

value: meiosis hour 4


title: e9.5_LA_1-D12

first: Guang

last: Li

address: 530 45th St. 8116 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
Basecalls performed using RTA (Real Time Analysis. v1.18)
Sequenced reads were demutiplexed, and mapped to mouse genome GRCm38.79 with STAR 2.4.0
The mapped reads of each gene were counted with HTSeq, and TPM were calculated with R script.
Genome_build: GRCm38.79
Supplementary_files_format_and_content: tab-delimited text files include counts number for each gene in each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: e9.5 left atrium

extract_protocol:
Mouse embryonic hearts derived single cells were captured, lysed, and pre-amplified in C1 microfluidic chips.
RNA libraries were prepared with Nextera XT reagent for illumina sequencing

tag: strain

tag: developmental stage

tag: tissue

value: left atrium


title: e9.5_LA_1-D10


title: e9.5_LA_1-D7


title: Batch 2_time point 4_2

value: meiosis hour 6


title: Batch 2_time point 3_1


title: Batch 2_time point 5_1

value: meiosis hour 8


title: Batch 2_time point 5_2


title: e9.5_LA_1-C9


title: e9.5_LA_1-C7


title: Batch 2_time point 2_1


title: e9.5_LA_1-E11


title: e9.5_LA_1-C6


title: Batch 2_time point 1_1


title: e9.5_LA_1-C8


title: e9.5_LA_1-E9


title: e9.5_LA_1-D11


title: e9.5_LA_1-F3


title: e9.5_LA_1-D5


title: e9.5_LA_1-D1


title: Batch 2_time point 4_1


title: e9.5_LA_1-D3


title: Batch 1_time point 4


title: Batch 1_time point 2


title: e9.5_LA_1-C12


title: Batch 1_time point 6


title: e9.5_LA_1-C4


title: e9.5_LA_1-C5


title: Batch 1_time point 1


title: Batch 1_time point 3


title: e9.5_LA_1-C3


title: e9.5_LA_1-C10


title: e9.5_LA_1-B9


title: e9.5_LA_1-B8


title: e9.5_LA_1-B7


title: e9.5_LA_1-B3


title: e9.5_LA_1-C11


title: e9.5_LA_1-B5


title: Batch 1_time point 5


title: e9.5_LA_1-C1


title: e9.5_LA_1-B4


title: e9.5_LA_1-A7


title: e9.5_LA_1-B12


title: e9.5_LA_1-A9


title: e9.5_LA_1-B1


title: e9.5_LA_1-B10


title: e9.5_LA_1-A5


title: e9.5_LA_1-A8


title: e9.5_LA_1-A6


title: e9.5_LA_1-B11


title: e9.5_LA_1-A3


title: e9.5_LA_1-A11


title: e9.5_LA_1-C2


title: e9.5_LA_1-A10


title: e9.5_LA_1-A1


title: e9.5_LA_1-A4


title: e9.5_LA_1-A2


title: e9.5_LA_1-A12


title: SuRE BAC library K562 cDNA, Biorep2

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description:
K562_BAC_SuRE34_BioRep2
quantification of barcodes in cDNA
SuRE-counts-BAC.txt.gz
sure34.k562.norm.plus.160718.bw
sure34.k562.norm.minus.160718.bw

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2000, Illumina HiSeq 2500, or Illumina MiSeq.
For plasmid library and cDNA samples the barcode sequence was extracted from the read  (using cutadapt and custom scripts) and counted.
For iPCR samples the barcode and the gDNA was extracted from the paired-end reads (using cutadapt and custom scripts). gDNA was then aligned to the reference genome (using bowtie2). Barcodes were then associated with genomic regions.
All replicate samples were pooled.
For each region identified in the iPCR data a normalized SuRE expression value was calculated as the ratio of the total readcount in the cDNA samples and the total readcount in the plasmid library samples plus a pseudocount of 1.
Genome_build: hg19
Supplementary_files_format_and_content: .txt and .wig files were generated using custom R-scripts

organism: Homo sapiens

source_name: cell line K562

growth_protocol: K562 (ATCC® CCL-243™) were cultured according to supplier's protocol.

extract_protocol: RNA was isolated using Trisure (#BIO-38032; Bioline) and polyA RNA was purified using Oligotex from Qiagen (#70022; Qiagen). PolyA RNA was divided into 10 µl reactions containing 500 ng RNA and DNase treated with  10 units for 30 minutes (#04716728001; Roche) and DNase was inactivated by addition of 1µl 25mM EDTA and incubation at 70ºC for 10 minutes. Next, cDNA was produced by first adding 1 µl of 10 mM gene specific primer targeting the GFP ORF (247JvA) and 1 µl dNTP (10mM each) and incubating for 5 minutes at 65°C. Then 4 µl of RT buffer, 20 units RNase inhibitor (#EO0381; ThermoFisher Scientific), 200 units of  Maxima reverse transcriptase (#EP0743; ThermoFisher Scientific)  and 2.5 µl water was added and the reactionmix was incubated for 30 minutes at 50°C followed by heat-inactivation at 85° for 5 minutes. Per biological replicate, 20-30 reactions were done in parallel. Each 20 µl reaction was then PCR amplified (1’ 96 °C, 20x(15’’ 96 °C, 15’’ 60 °C, 15’’ 72 °C)) in a 100 µl reaction with MyTaq™ Red Mix and primers 151AR (containing the S1 and p5 adapter) and (index variants of) 211JvA (containing the S2, index and p7 adapter) for 21 cycles. Reactions were then pooled and 500 µl was purified using a PCR purification kit (#BIO-52060) and then size-selected using e-gel (#G6400EU; Invitrogen) and subjected to single read 50 bp high throughput sequencing on an Illumina HiSeq2000 or HiSeq2500.

treatment_protocol: 3 biological replicates (i.e. transfection replicates) were done separately of 50 million cells and harvested after 24 hours. Cells were transiently transfected using Amaxa Nucleofector II, program T-016 and nucleofection buffer as published previously (Hendel, A. et al,  Cell Rep 7, 293-305, 2014).

tag: cell line

tag: cell type

value: erythroleukemia


title: SuRE BAC library K562 cDNA, Biorep1

description:
K562_BAC_SuRE34_BioRep1
quantification of barcodes in cDNA
SuRE-counts-BAC.txt.gz
sure34.k562.norm.plus.160718.bw
sure34.k562.norm.minus.160718.bw


title: BAC plasmid library, PCR rep1

description:
Sce1_plDNA_BAC_SuRE34_PCRrep1
quantification of barcodes in cDNA
SuRE-counts-BAC.txt.gz
sure34.k562.norm.plus.160718.bw
sure34.k562.norm.minus.160718.bw


title: iPCR, sequencing lane 1

description:
iPCR SuRE34
iPCR for barcode-to-fragment association
SuRE-counts-BAC.txt.gz
sure34.flat.ipcr.coverage.160503.bw

library_source: genomic

molecule: genomic DNA

extract_protocol: To find out which barcodes were associated with which genomic fragments, we digested 4 µg SuRE library with I-CeuI (#R0699S; NEB), followed by magnetic bead purification (1:1 ratio beads:DNA solution). Of this, 2 µg was self-ligated overnight at 16 °C in a total volume of 2 ml (#10799009001 Roche), and purified using phenol-chloroform extraction and isopropanol precipitation. To reduce the size of the genomic fragments this material was digested for 1 hour with 10 units of frequent cutter Nla III (#R0125S; NEB) or 10 units of HpyCH4V (#R0620L; NEB), bead purified and self-ligated again in a final volume of 1 ml. This material was purified by phenol-chloroform extraction and isopropanol precipitation, treated with 25 units of Plasmid-Safe™ ATP-Dependent DNase for 1 hour and purified again with phenol-chloroform and isopropanol precipitation. To facilitate PCR, the resulting mini-circles were linearized by digesting with I-SceI (#R0694S; NEB) in a volume of 25 µl. Finally, 10 cycles of PCR (1¢ at 98°C, 10x(15¢ at 98°,15¢ at 60°, 20¢ at 72°)) with Phusion high-fidelity DNA Polymerase (#M0530L; NEB) were performed on 2.5 µl of the I-SceI digested material using primers 151AR (containing the S1 and p5 adapter) and (index variants of) 117JvA (containing the S2, index and p7 adapter). The PCR product was bead purified and subjected to high-throughput paired-end sequencing on an Illumina MiSeq, HiSeq2000 or HiSeq2500.


title: BAC plasmid library, PCR rep2

description:
Sce1_plDNA_BAC_SuRE34_PCRrep2
quantification of barcodes in cDNA
SuRE-counts-BAC.txt.gz
sure34.k562.norm.plus.160718.bw
sure34.k562.norm.minus.160718.bw


title: iPCR, SuRE23

description:
iPCR SuRE23, sequencing lane 1, 2, 3, 4
iPCR for barcode-to-fragment association
SuRE-counts-K562.txt.gz
SuRE23.iPCR.flat.count.160502.bw


title: primary lung tumor-drived cells [3953_12_KTS046_CTTGTAA]

status: Public on Nov 09 2016

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

institute: NKI

description: 3953_12_KTS046_CTTGTAA_S84_L008_R1_001.fastq.gz

data_processing:
tuxedo-counts: Tophat, bamqc, icount, eset, QCstrandness
Tophat version: 2.0.12
Bowtie version: 1.1.0
Samtools version: 0.1.19
DEseq2
Genome_build: mus_musculus.NCBIM37.67.dna.toplevel
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each Sample

source_name: primary lung tumor-drived cells

extract_protocol:
EAF fixed and paraffin embedded tissues
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocols.

treatment_protocol: Mice conditionally overexpressing Sox2 in combination with the biallelic inactivation of Cdkn2ab and Pten were Ad-K14-Cre intratracheally injected to develop SCC from basal cells of tracheobronchial epithelium

tag: disease state

value: primary mouse NSCLC

tag: genotype/variation

value: Sox2/+; Pten-/-;Cdkn2ab-/-

tag: cancer subtype

value: Squamous cell carcinoma (SCC)

value: lung


title: primary lung tumor-drived cells [3953_13_KTS093_AGTCAAC]

description: 3953_13_KTS093_AGTCAAC_S85_L008_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_7_16GFE017_CGATGTA]

description: 3953_7_16GFE017_CGATGTA_S79_L007_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_10_16GFE019_GCCAATA]

description: 3953_10_16GFE019_GCCAATA_S82_L008_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_2_15GFE021_GTTTCGG]

description: 3953_2_15GFE021_GTTTCGG_S74_L007_R1_001.fastq


title: primary lung tumor-drived cells [3953_6_16GFE003_ATTCCTT]

description: 3953_6_16GFE003_ATTCCTT_S78_L007_R1_001.fastq


title: primary lung tumor-drived cells [3953_5_16GFE001_ACTGATA]

description: 3953_5_16GFE001_ACTGATA_S77_L007_R1_001.fastq


title: primary lung tumor-drived cells [3953_14_KP088_AGTTCCG]

description: 3953_14_KP088_AGTTCCG_S86_L008_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_4_15GFE028_GAGTGGA]

description: 3953_4_15GFE028_GAGTGGA_S76_L007_R1_001.fastq


title: primary lung tumor-drived cells [3953_11_16GFE020_CAGATCA]

description: 3953_11_16GFE020_CAGATCA_S83_L008_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_9_16GFE011_ACAGTGA]

description: 3953_9_16GFE011_ACAGTGA_S81_L008_R1_001.fastq.gz


title: primary lung tumor-drived cells [3953_3_15GFE024_CGTACGT]

description: 3953_3_15GFE024_CGTACGT_S75_L007_R1_001.fastq


title: primary lung tumor-drived cells [3953_1_15GFE019_GTGGCCT]

description: 3953_1_15GFE019_GTGGCCT_S73_L007_R1_001.fastq


title: 9th-C9_S13

city: Farmington

first: Michael

last: Stitzel

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Sequencing, Read Mapping, and Quality Control. All sequencing was performed on a NextSeq500 (Illumina) using the 75 cycle high output chip. RNA-seq reads were subjected to quality control using custom scripts developed at the computational sciences group at The Jackson Laboratory. Briefly, reads with more than 30% of bases with quality scores were removed from the analysis and samples with more than 50% reads removed are removed from further analysis. Trimmed reads were mapped to human transcriptome (GRCh37, ensemble v70) using Bowtie2 (Langmead and Salzberg, 2012) and expression levels of all genes were estimated using RSEM (Li and Dewey, 2011). Transcript per million (TPM) values as defined by RSEM were added a value of 1 (to avoid zeros) prior to log2 transformation.
Single Cell Sample Processing and Quality Filtering. 26,616 protein-coding genes and long non-coding RNAs (lincRNAs) from the GRCh37, ensemble v70 build were used in our study. Genes with expression levels greater than or equal to 5 TPM in a sample were considered to be expressed. 72 single cell samples that expressed fewer than 3500 genes according to these criteria were removed from downstream analysis. Approximately one-third (340/978, or 35%) of cells expressed more than one marker gene; these were removed from subsequent analysis owing to concerns that these were the result of two vertically stacked cells in a given capture site. Ultimately, there are 638 samples comprising this processed dataset.
Islet Cell Type Classification. In general, density plots of marker gene expression in our samples portray a bimodal distribution. Therefore, Gaussian mixture modeling was fitted on a per gene basis using two mixture components to identify in which samples each gene was expressed. This Gaussian mixture modeling was performed using the R-package, mclust_5.2 (Fraley et al. 2016). Each single cell sample was classified as a specific pancreatic cell type if and only if a single gene from the selected marker gene list: INS (beta), GCG (alpha), SST (delta), PPY (gamma/PP), KRT19 (ductal), PRSS1 (acinar), and COL1A1 (stellate) was expressed in the sample and none of the other marker genes were expressed. If more than one of these marker genes were expressed in a single cell, it was given the label  “multiple”. If none of the marker genes were expressed it was labeled as “none”.
Genome_build: GRCh37, ensembl v70
Supplementary_files_format_and_content: Comma-separated value file contains raw transcript per million (TPM) values of 26,616 protein coding and long non-coding RNAs. The files are matrices with rows representing features (genes) and columns representing samples (638 total).

source_name: Pancreatic Islet

growth_protocol: Islet Acquisition, Processing, and Dissociation. Islets have been acquired through IIDP and shipped in Prodo-media overnight on cold packs, washed and taken into 37oC 5% CO2 Prodo-media culture immediately after arrival. Twenty-four hours after taken into culture an adequate volume of islets (500IEq) was aliquoted and centrifuged at 180xg 3min @RT. The first aliquot (100IEq) was straight flash frozen (= baseline), the second aliquot (200IEq) was resuspend in 1ml Prodo-media (= bulk) and the third aliquot (200IEq) resuspend in 1ml Accutase (Innovative Cell Technologies, Inc.) (= single cell) and incubated for 10min @37oC water bath, with pipetting every 2min. The second aliquot in Prodo-media was divided (100IEq each) and kept one @RT and one on ice. While the Accutase sample was put through pre-wet cell strainer (BD) and rinsed with 9ml pre-warmed CMRL+10%FBS media to stop reaction and centrifuged at 180xg 3min @RT. Dissociated cells were measured in 300ul CMRL+10%FBS media on a Countess II FL (Thermo Fisher Scientific) to assess cell number and viability and diluted down to 300 cells/ul. Total processing and handling time for each islet was ≤60 minutes.

extract_protocol:
Single Cell Processing on the C1 Single Cell Autoprep System. After enumeration, cells were diluted to a final concentration range of 250–400 cells per μl and 5 ul loaded onto each C1 integrated fluidic circuit (IFC; 10- to 17-μm chip) for cell capture on the C1 Single-cell Auto Prep System.
After capture cells were imaged within each capture nest with an EVOS FL Auto microscope (Life Technologies). IFCs were subsequently loaded with additional reagents for subsequent cell lysis, and SMARTer v1-based (Clontech), olio-(dT)-primed reverse transcription, template switching for second strand priming, and amplification of cDNA on the C1 System. Qualitative and quantitative analysis of all single cell cDNA products was performed on a 96 capillary Fragment Analyzer (Advanced Analytical). Only cell singlets, as determined by imaging, with adequate cDNA yield and quality were processed for subsequent sequencing. Fragmentation and tagmentation of cDNA was done with Nextera XT regarent (Illumina) using dual indices to prepare single-cell multiplexed libraries.

value: Alpha

value: Pancreatic Islet

tag: Sex

value: Female

tag: disease

value: Non-Diabetic

tag: age

tag: race

value: White

tag: bmi

tag: islet unos id


title: primary lung tumor-drived cells_6

description: 3463_6_15GFE028_big_AGATGTAC_L001_R1_001.fastq.gz

treatment_protocol: Mice conditionally overexpressing Sox2 in combination with the biallelic inactivation of Cdkn2ab and Pten were Ad-K14-Cre intratracheally injected to develop SCC from basal cells of tracheobronchial epithelium. All mouse samples in this series were Ad5-K14-Cre induced.

value: SCC

tag: genotype


title: primary lung tumor-drived cells_4

description: 3463_4_15GFE024_ACACGACC_L001_R1_001.fastq.gz


title: primary lung tumor-drived cells_5

description: 3463_5_15GFE028_small_ACAGATTC_L001_R1_001.fastq.gz


title: 9th-C96_S81

value: None/Other


title: primary lung tumor-drived cells_3

description: 3463_3_15GFE021_big_AATGTTGC_L001_R1_001.fastq.gz


title: primary lung tumor-drived cells_2

description: 3463_2_15GFE021_small_AATCCGTC_L001_R1_001.fastq.gz


title: 9th-C93_S76

value: Beta


title: primary lung tumor-drived cells_1

description: 3463_1_15GFE019_AAGGACAC_L001_R1_001.fastq.gz


title: 9th-C94_S83


title: 9th-C92_S77


title: 9th-C91_S78


title: 9th-C8_S14


title: primary lung tumor-drived cells [3953_8_16GFE018_TGACCAA]

description: 3953_8_16GFE018_TGACCAA_S80_L008_R1_001.fastq.gz


title: 9th-C89_S72


title: 9th-C88_S73


title: 9th-C86_S67


title: 9th-C83_S61


title: 9th-C77_S53


title: 9th-C75_S47


title: 9th-C80_S56


title: 9th-C79_S57

value: Gamma/PP


title: 9th-C74_S48


title: 9th-C6_S7


title: 9th-C81_S55


title: 9th-C84_S60

value: Ductal


title: 9th-C65_S32


title: 9th-C67_S37


title: 9th-C69_S39


title: 9th-C62_S26


title: 9th-C64_S31


title: 9th-C66_S33


title: 9th-C70_S42


title: 9th-C85_S68


title: 9th-C61_S25


title: 9th-C52_S10


title: 9th-C51_S6


title: 9th-C59_S20


title: 9th-C57_S16


title: 9th-C5_S8


title: 9th-C49_S4


title: 9th-C87_S66


title: 9th-C40_S69


title: 9th-C41_S70


title: 9th-C3_S1


title: 9th-C36_S59


title: 9th-C29_S51


title: 9th-C2_S2

value: Stellate


title: 9th-C30_S52


title: 9th-C25_S45


title: 9th-C28_S50

value: Delta


title: 9th-C22_S41


title: 9th-C20_S35


title: 9th-C19_S36


title: 9th-C17_S29


title: 9th-C1_S3


title: 9th-C15_S22


title: 9th-C13_S24


title: 9th-C16_S30


title: 9th-C11_S17


title: 9th-C10_S18


title: 9th-C46_S79


title: 9th-C14_S23


title: 8th-C90_S152

value: Male

value: African American


title: 8th-C91_S158


title: 8th-C79_S140


title: 8th-C87_S148


title: 8th-C92_S157


title: 8th-C7_S95


title: 8th-C85_S150


title: 8th-C84_S143


title: 9th-C38_S64


title: 8th-C75_S128


title: 8th-C70_S123


title: 8th-C74_S129


title: 8th-C67_S117


title: 8th-C6_S88


title: 8th-C64_S112


title: 8th-C61_S107


title: 8th-C59_S102


title: 8th-C58_S101


title: 8th-C47_S160


title: 8th-C57_S98


title: 8th-C94_S162


title: 8th-C69_S119


title: 8th-C65_S113


title: 8th-C38_S147


title: 8th-C34_S141


title: 8th-C37_S146


title: 8th-C95_S161


title: 8th-C55_S96


title: 8th-C2_S85


title: 8th-C26_S126


title: 8th-C20_S116


title: 8th-C24_S120


title: 8th-C23_S121


title: 8th-C21_S115


title: 8th-C11_S99


title: 8th-C73_S130


title: 8th-C28_S131


title: 8th-C18_S110


title: 7th-C96_S82


title: 7th-C90_S73


title: 7th-C94_S83


title: 7th-C8_S13


title: 8th-C44_S155


title: 7th-C85_S69


title: 7th-C88_S75


title: 7th-C81_S56


title: 7th-C89_S74


title: 7th-C84_S62


title: 7th-C80_S57


title: 7th-C82_S64


title: 7th-C77_S51


title: 7th-C69_S39


title: 7th-C76_S52


title: 7th-C73_S47


title: 7th-C72_S42


title: 7th-C68_S38


title: 8th-C10_S100


title: 7th-C65_S32


title: 7th-C62_S27


title: 7th-C53_S10


title: 7th-C56_S15


title: 7th-C60_S22


title: 7th-C58_S20


title: 7th-C59_S21


title: 7th-C57_S16


title: 7th-C64_S31


title: 7th-C52_S9


title: 7th-C79_S58


title: 7th-C50_S5


title: 7th-C4_S8


title: 7th-C47_S81


title: 7th-C45_S77


title: 7th-C3_S1


title: 7th-C40_S70


title: 7th-C34_S59


title: 7th-C32_S54


title: 7th-C66_S33


title: 7th-C31_S53


title: 7th-C28_S48


title: 7th-C25_S43


title: 7th-C2_S2


title: 7th-C20_S35


title: 7th-C24_S40


title: 7th-C1_S3


title: 7th-C49_S4


title: 7th-C36_S61


title: 7th-C44_S76

value: Acinar


title: 7th-C17_S29


title: 7th-C19_S36


title: 7th-C21_S34


title: 6th-C75_S46


title: 6th-C79_S60


title: 6th-C9_S12


title: 6th-C87_S70


title: 6th-C80_S59


title: 7th-C12_S17


title: 6th-C90_S76


title: 6th-C89_S77


title: 7th-C11_S18


title: 7th-C15_S23


title: 6th-C91_S84


title: 6th-C85_S72


title: 7th-C10_S19


title: 6th-C83_S65


title: 6th-C82_S66


title: 7th-C14_S24


title: 6th-C84_S64


title: 6th-C67_S36


title: 6th-C66_S32


title: 6th-C5_S8


title: 6th-C62_S25


title: 6th-C63_S26


title: 6th-C73_S48


title: 6th-C71_S41


title: 6th-C64_S30


title: 6th-C65_S31


title: 6th-C93_S82


title: 6th-C77_S53


title: 6th-C59_S21


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title: 6th-C30_S51


title: 6th-C23_S38


title: 6th-C25_S43


title: 6th-C53_S10


title: 6th-C21_S33


title: 6th-C34_S61


title: 6th-C2_S2


title: 6th-C42_S75


title: 6th-C28_S49


title: 6th-C22_S39


title: 6th-C24_S37


title: 6th-C54_S11


title: 6th-C19_S35


title: 6th-C1_S3


title: 5th-C90_S115


title: 5th-C92_S124


title: 6th-C20_S34


title: 5th-C9_S92


title: 6th-C29_S50


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title: 6th-C51_S6


title: 6th-C16_S29


title: 5th-C88_S117


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title: 5th-C81_S115


title: 5th-C83_S111


title: 6th-C40_S73


title: 5th-C87_S119


title: 5th-C80_S116


title: 5th-C7_S93


title: 5th-C70_S103


title: 5th-C73_S111


title: 5th-C74_S110


title: 5th-C6_S84


title: 5th-C67_S105


title: 5th-C69_S107


title: 5th-C59_S94


title: 5th-C56_S95


title: 5th-C58_S93


title: 5th-C49_S89


title: 5th-C57_S96


title: 5th-C54_S89


title: 5th-C50_S90


title: 5th-C42_S114


title: 5th-C41_S113


title: 5th-C43_S121


title: 5th-C47_S118


title: 5th-C5_S85


title: 5th-C40_S112


title: 5th-C35_S109


title: 5th-C34_S108


title: 5th-C30_S105


title: 5th-C25_S108


title: 5th-C77_S107


title: 5th-C68_S106


title: 5th-C64_S99


title: 5th-C66_S101


title: 5th-C45_S123


title: 5th-C18_S96


title: 5th-C16_S98


title: 5th-C12_S90


title: 5th-C14_S97


title: 5th-C10_S92


title: 4th-C93_S88

value: Type 2 Diabetic

value: Hispanic


title: 4th-C9_S13

value: Alpha


title: 4th-C95_S95

value: Pancreatic Islet


title: 4th-C96_S94


title: 4th-C92_S89


title: 4th-C94_S96


title: 5th-C11_S91

value: Female


title: 4th-C8_S14


title: 4th-C89_S83


title: 4th-C86_S77


title: 4th-C81_S64


title: 4th-C83_S71


title: 4th-C80_S65


title: 4th-C87_S76


title: 4th-C82_S72


title: 4th-C7_S15


title: 4th-C79_S66


title: 5th-C21_S102

value: Non-Diabetic


title: 4th-C78_S58


title: 4th-C75_S52


title: 5th-C19_S104

value: White


title: 4th-C70_S46


title: 4th-C73_S54


title: 4th-C68_S41


title: 4th-C67_S40


title: 4th-C69_S42


title: 4th-C66_S36


title: 4th-C88_S84


title: 4th-C5_S8


title: 4th-C63_S30


title: 4th-C85_S78


title: 4th-C59_S23


title: 4th-C50_S5


title: 4th-C62_S29


title: 4th-C57_S18


title: 4th-C51_S6


title: 4th-C56_S17


title: 4th-C4_S9


title: 4th-C49_S4


title: 4th-C40_S79


title: 4th-C43_S85


title: 4th-C3_S1


title: 4th-C33_S63


title: 4th-C35_S68


title: 4th-C36_S69


title: 4th-C37_S73


title: 4th-C32_S62


title: 4th-C27_S51


title: 4th-C28_S55


title: 4th-C24_S43


title: 4th-C29_S56


title: 4th-C23_S44


title: 4th-C26_S50


title: 4th-C22_S45


title: 4th-C64_S34


title: 4th-C14_S26


title: 4th-C18_S31


title: 4th-61_S28


title: 3rd-C9_S5


title: 4th-C12_S19


title: 3rd-C95_S81


title: 3rd-C91_S91


title: 4th-C45_S87


title: 3rd-C85_S83


title: 3rd-C86_S85


title: 3rd-C84_S75


title: 3rd-C82_S11


title: 3rd-C92_S86


title: 3rd-C85_S79


title: 3rd-C88_S24


title: 3rd-C79_S67


title: 3rd-C71_S80


title: 3rd-C6_S44


title: 3rd-C7_S40


title: 3rd-C87_S88


title: 3rd-C76_S22


title: 3rd-C69_S78


title: 3rd-C68_S13


title: 3rd-C61_S64


title: 3rd-C63_S54


title: 3rd-C60_S10


title: 3rd-C67_S69


title: 3rd-C96_S79


title: 3rd-C59_S91


title: 3rd-C65_S20


title: 3rd-C58_S3


title: 3rd-C56_S90


title: 3rd-C53_S67


title: 3rd-C51_S87


title: 3rd-C57_S5


title: 3rd-C4_S25


title: 3rd-C49_S60


title: 3rd-C46_S93


title: 3rd-C47_S35


title: 3rd-C44_S32


title: 3rd-C40_S57


title: 3rd-C3_S2


title: 3rd-C42_S74


title: 3rd-C36_S2


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title: 3rd-C26_S28


title: 3rd-C23_S94


title: 3rd-C20_S22


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title: 3rd-C52_S86


title: 3rd-C1_S39


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title: 2nd-C94_S96


title: 2nd-C95_S95


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title: 2nd-C93_S88


title: 2nd-C86_S77


title: 2nd-C83_S71


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title: 10th_C56_S74


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title: 10th_C54_S124


title: 10th_C51_S80


title: 10th_C50_S73


title: 10th_C4_S103


title: 10th_C46_S94


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title: 10th_C37_S49


title: 10th_C34_S92


title: 10th_C31_S48


title: 10th_C32_S56


title: 10th_C33_S64


title: 10th_C24_S90


title: 10th_C28_S91


title: 10th_C19_S62


title: 10th_C23_S98


title: 10th_C17_S97


title: 10th_C30_S107


title: 10th_C1_S59


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title: 10th_C10_S104


title: 10th_C13_S61


title: Untreated-Ctrl-05222015_S7

data_processing:
Sequencing, Read Mapping, and Quality Control. All sequencing was performed on a NextSeq500 (Illumina) using the 75 cycle high output chip. RNA-seq reads were subjected to quality control using custom scripts developed at the computational sciences group at The Jackson Laboratory. Briefly, reads with more than 30% of bases with quality scores were removed from the analysis and samples with more than 50% reads removed are removed from further analysis. Trimmed reads were mapped to human transcriptome (GRCh37, ensemble v70) using Bowtie2 (Langmead and Salzberg, 2012) and expression levels of all genes were estimated using RSEM (Li and Dewey, 2011). Transcript per million (TPM) values as defined by RSEM were added a value of 1 (to avoid zeros) prior to log2 transformation.
Genome_build: GRCh37, ensembl v70
Supplementary_files_format_and_content: Comma-separated value file contains raw transcript per million (TPM) values of 26,616 protein coding and long non-coding RNAs. The files are matrices with rows representing features (genes) and columns representing samples. There are 24 total bulk islet samples in this processed file.

extract_protocol:
Bulk cells were pelleted and RNA purified using the PicoPure RNA isolation kit (Life Technology).
All RNA-seq libraries from bulk sample RNA were generated with the same SMARTer v1 chemistry (Clontech) as the C1 single cell data largely following manufacturers instructions. Unlike the C1 workflow, after first strand DNA synthesis cDNA was purified using Agencourt AMPure beads (Beckman Coulter). cDNA was subsequently amplified through 12 PCR cycles. The cDNA yield and fragment size was measured on a 2100 Bioanalyzer (Agilent). For sequencing library preparation, amplified cDNA was sheared using a Covaris LE220 system to obtain fragments of approximately 200 bp. The fragmented cDNA was prepared for sequencing using the NEBNext DNA Library Prep Kit for Illumina sequencing (New England Biolabs).

tag: bulk sample type

value: Intact

value: Non-diabetic


title: 10th_C11_S96

value: Beta


title: Untreated-Ctrl-05202015_S2


title: 10th_C45_S66


title: Untreated-Ctrl-03272015_S9

value: Type 2 diabetic


title: Untreated-Ctrl-03182015_S3


title: undissociated-c1-ctrl-10292015_S18


title: undissociated-c1-ctrl-10012015_S13


title: undissociated-c1-ctrl-09102015_S8


title: undissociated-c1-ctrl-09032015_S3


title: Single-cell-bulk-c1-10292015_S20

value: Dissociated


title: Single-cell-bulk-c1-10012015_S15


title: Single-cell-bulk-c1-09102015_S10


title: Single-cell-bulk-c1-09032015_S5


title: 10th_C20_S54


title: Single-cell-bulk-05222015_S8


title: Single-cell-bulk-05202015_S3


title: ATAC_N_4DPT

city: Dallas

first: Derek

middle: K

last: Smith

state: Texas

address: 5323 Harry Hines Blvd, NA5.202

department: Molecular Biology

institute: The University of Texas Southwestern Medical Center

data_processing:
Genome_build: GRCh37/hg19
Reads were aligned to the human reference sequence GRCh37/hg19 with the Bowtie algorithm (version 1.0.0). Peak calling, peak‑gene annotation, motif discovery (parameter: 200 nucleotide window from peak center), and generation of heatmap matrices were performed using HOMER (version 4.7). The UCSC Genome Browser was used to visualize tag densities and multi-experiment datasets.
Supplementary_files_format_and_content: Alignment files (.bam) were generated using Bowtie (version 1.0.0). UCSC.bedGraph and peak files (.txt) were generated using HOMER (version 4.7)

source_name: Fetal Lung Fibroblast

growth_protocol: MRC-5 fibroblasts were cultured in Dulbecco’s modified eagle medium (DMEM, GE Healthcare, SH30243.01) supplemented with 15% (v/v) fetal bovine serum (Corning, 35-010-CV) and 1% (v/v) penicillin-streptomycin (GE Healthcare, SV30010). Fibroblasts were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
MRC-5 fibroblasts were cultured, transduced with GFP-encoding, NEUROG2-encoding or NEUROG2+SOX4-shRNA-encoding lentivirus, and treated with DMEM containing 15% fetal bovine serum, neuron induction medium or neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin for 4 days, respectively. Approximately 5×106 cells were treated with Accutase cell detachment solution (Innovative Cell Technologies) for 3 minutes and collected in ice-cold PBS by centrifugation (525 × g, 5 minutes, 4°C). Cells were resuspended by repeated gentle pipetting in 2 ml ice-cold resuspension buffer (PBS containing 25 mM HEPES (pH 7.0) and 5 mM EDTA). GFP expressing viable cells were isolated using fluorescence-based sorting on a MoFlo platform (Beckman Coulter). Exactly 50,000 cells were sorted into lysis buffer (10 mM Tris (pH 7.5), 10 mM NaCl, 3 mM MgCl2, and 0.1% (v/v) IGEPAL CA 630) at 4°C then collected by centrifugation (21,130 × g, 2 minutes, 4°C). The pellet was resuspended in 50 μl transposition mix (25 μl 2X TD buffer, 22.5 μl nuclease-free H2O, and 2.5 μl Nextera Tn5 transposase (Illumina, FC-121-1030)) and incubated exactly 30 minutes at 37°C with gentle agitation (400 rpm). Chromatin was purified with a MinElute PCR purification kit (Qiagen, 28004) and twice eluted in 10 μl elution buffer.
Amplification reactions of 20 μl eluted chromatin, 2.5 μl universal ATAC primer (25 μM, Appendix 4), 2.5 μl barcoded ATAC primer (25 μM, Appendix 4), and 25 μl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, M0541S) were amplified for 1 cycle (5 minutes, 72°C) followed by 5 cycles (10 seconds, 98°C; 30 seconds, 63°C; 1 minute, 72°C). To determine the number of additional amplification cycles required, quantitative real-time PCR using 5 μl ATAC library reaction, 2.5 μl NEBNext High-Fidelity 2X PCR Master Mix, 0.125 μl universal ATAC primer (25 μM), 0.125 μl barcoded ATAC primer (25 μM), and 2 μl 5X SYBR Green I (ThermoFisher Scientific, S7563) was performed for 1 cycle (30 seconds, 98°C) followed by 20 cycles (10 seconds, 98°C; 30 seconds, 63°C; 1 minute, 72°C). The appropriate number of additional amplification cycles was determined for each library (11 total cycles) and amplified libraries were purified with a MinElute PCR purification kit then eluted in 20 μl elution buffer. Right side size selection with 0.4X Agencourt AMPure XP beads (Beckman Coulter, A63881) was used to reduce fragments larger than 1,000 nucleotides and left side size selection with 1X Agencourt AMPure XP beads was used to eliminate fragments smaller than 150 nucleotides. Fragment length and size selection were evaluated after library amplification using a high-sensitivity DNA analysis kit (Agilent Technologies, 5067-4626). Library quantification prior to flow cell loading was performed using bioanalyzer traces and a Quant-iT PicoGreen dsDNA assay kit (ThermoFisher Scientific, P11496).
ATAC-seq: single end 50-base length sequencing reads were generated on an Illumina HiSeq 2500 System.

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.8×10^6 cells in a 10 cm polystyrene dish. Fibroblasts were transduced with HA-NEUROG2-encoding lentivirus 24 hours after plating. The optimal lentivirus titer was empirically determined (4-fold dilution for 10 ml-capacity 10 cm dishes) and consistently yielded ≥90% TUBB3-positive and MAP2-positive neurons. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025).

value: MRC-5 (ATCC, CCL-171)

tag: transduced with (factor)

tag: supplemented with (medium and small molecules)

value: Neuron induction medium

tag: atac-seq performed (#) days post treatment with small molecules

value: 4 DPT


title: Single-cell-bulk-03272015_S10

tag: tissue

value: Male


title: baseline-10292015_S17

value: Baseline


title: ATAC_NFD+SOX4shRNA_4DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.8×10^6 cells in a 10 cm polystyrene dish. Fibroblasts were transduced with HA-NEUROG2+SOX4-shRNA-encoding lentivirus 24 hours after plating. The optimal lentivirus titer was empirically determined (4-fold dilution for 10 ml-capacity 10 cm dishes) and consistently yielded ≥90% TUBB3-positive and MAP2-positive neurons. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) supplemented with 10 μM forskolin (Sigma-Aldrich, F6886) and 1 μM dorsomorphin (Millipore, 171260) 48 hours post infection.

tag: cell line

value: Neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin


title: K562__8h__rep1

city: Cambridge

first: MARTA

last: MELE

state: MA

address: 7 divinity avenue

department: Harvard Stem Cells and Regenerative Biology

institute: Harvard University

data_processing:
Reads were mapped to the hg19 reference genome using Bowtie v2.2.5 and TopHat v2.0.14 with the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode v19.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, against a reference transcriptome based on Gencode v19.
Processed data files report cufflinks gene quantifications.
Genome_build: hg19
Supplementary_files_format_and_content: processed data files contain per-replicate gene expression levels (FPKM) for  genes annotated in gencode 19 including lncRNAs and mRNAs.

growth_protocol: K-562 cells were cultured in RPMI 1640 supplemented with 10% FBS and 1X antibiotic-antimycotic in 75 cm2 flasks. HUES9 cells were cultured under feeder-free conditions in  mTeSR1 medium in Geltrex coated 6-wells plates.

extract_protocol:
TRIzol/chloroform extraction followed by spin-column purification (RNeasy Mini kit, Qiagen)
TruSeq RNA Sample Preparation Kit v2, Illumina
76 bp paired-end

treatment_protocol: actinomycin D (5 μg/ml medium)

tag: agent

value: actD

tag: time

value: 8 hours since actD treatment


title: K562__8h__rep2


title: ATAC_NFD_4DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.8×10^6 cells in a 10 cm polystyrene dish. Fibroblasts were transduced with HA-NEUROG2-encoding lentivirus 24 hours after plating. The optimal lentivirus titer was empirically determined (4-fold dilution for 10 ml-capacity 10 cm dishes) and consistently yielded ≥90% TUBB3-positive and MAP2-positive neurons. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) supplemented with 10 μM forskolin (Sigma-Aldrich, F6886) and 1 μM dorsomorphin (Millipore, 171260) 48 hours post infection.


title: ATAC_MRC5_4DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.8×10^6 cells in a 10 cm polystyrene dish. Fibroblasts were transduced with GFP-encoding lentivirus 24 hours after plating. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection and maintained in DMEM supplemented with 15% fetal bovine serum for the duration of culture.

value: Dulbecco’s modified eagle medium supplemented with 15% (v/v) fetal bovine serum


title: K562__8h__rep0


title: K562__4h__rep2

value: 4 hours since actD treatment


title: baseline-09102015_S7

value: Pancreatic Islet

value: Female


title: baseline-09032015_S2

value: African American


title: baseline-10012015_S12

value: White


title: K562__4h__rep1


title: K562__2h__rep2

value: 2 hours since actD treatment


title: baseline-05222015-Islet-16_S6

value: Non-diabetic


title: baseline-05202015-Islet-15_S1


title: K562__2h__rep1


title: K562__4h__rep0


title: K562__2h__rep0


title: baseline-03272015_S8

value: Type 2 diabetic

value: Hispanic


title: baseline-03182015_S2


title: K562__0.5h__rep2

value: 0.5 hours since actD treatment


title: K562__0.5h__rep1


title: K562__0.5h__rep0


title: Single-cell-bulk-03182015_S4

value: Dissociated


title: K562__0.0h__rep2

value: control

value: 0 hours since actD treatment


title: K562__0.0h__rep1


title: K562__0.0h__rep0


title: mESC_Nucleus_rep2

data_processing:
Reads were mapped to the hg19 reference genome using Bowtie v2.2.5 and TopHat v2.0.14 with the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode v19.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, against a reference transcriptome based on Gencode v19. The reference transcriptome contains all isoforms from gencode 19 but also it includes a full gene locus for each gene representing unprocessed/unspliced transcripts.
Processed data file reports cufflinks transcript quantifications. Quantifications include all gene isoforms and one isoform that extends the full gene loci and has the gene_id as transcript_id.
Genome_build: hg19
Supplementary_files_format_and_content: mESC_isoformExp_processed.txt contains per-replicate transcript expression levels (FPKM) for genes annotated in gencode 19 including lncRNAs and mRNAs. It also includes expression levels for the unprocessed transcripts (that is unspliced transcripts) which have the ensembl gene_id as identifier.

growth_protocol: Cells were grown in 2I+LIF media on previously-gelatinized 15 cm plates, at 37°C and 5% CO2, with daily media exchanges. Cells were passaged every 3–4 days by trypsinization.

extract_protocol:
RNA was harvested from cytoplasmic and nuclear fractions using Trizol-LS and Trizol reagents, respectively, following the manufacturer’s protocols. RNA was further purified by isopropanol precipitation and RNEasy purification with on-column DNAse treatment.
TruSeq RNA sample preparation kit, v2 (Illumina)
101 bp paired end

treatment_protocol: Harvested cells were hypotonically swollen and gently lysed with CHAPS detergent to yield a cytoplasmic fraction. The nuclear fraction was isolated by several isotonic washes and separation over a sucrose cushion.

tag: cell type

value: mESC

tag: cell fraction

value: nucleus


title: mESC_Nucleus_rep1


title: mESC_Cytoplasm_rep2

value: cytoplasm


title: mESC_Cytoplasm_rep1


title: HUES9__4h__rep2

value: actD


title: HUES9__8h__rep1

value: 8 hours since actD treatment


title: HUES9__8h__rep0


title: HUES9__8h__rep2


title: Immunoprecipitated mRNAs with control IgG

city: Nankoku

first: Keisuke

last: Taniuchi

address: Kohasu

country: Japan

institute: Kochi Medical School

description: library strategy: RIP-Seq

data_processing:
The data obtained, Illumina/Solexa reads from the IP (IGF2BP3) experiment and from the control (IgG) were mapped to the mRNAs from RefSeq using the LSKB Database. We approximate the density of each mRNA by the RPKM measure (Reads per kilobase per Million of mapped reads). We normalized RPKM estimates using adjusting the mean and standard deviation of each sample’s log2(RPKM) values.
IlluminaCASAVA ver.1.8.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SeqNovaTMCS (DNANexus).
We approximate the density of each mRNA by the RPKM measure (Reads per kilobase per Million of mapped reads) (Mortazavi A et al, Nat. Methods 5, 621-628, 2008). We normalized RPKM estimates using adjusting the mean and standard deviation of each sample’s log2(RPKM) values.
Supplementary_files_format_and_content: RPKM values for each Sample

source_name: pancreatic cancer

extract_protocol:
Fibronectin-stimulated S2-013 cells were lysed in NP2 buffer containing 50 mM Tris (pH 7.4), 150 mM NaCl, 1 mM MgCl2, 0.5% NP-40 and protease and RNAse inhibitors.
RIP protocol: Cell lysates were immunoprecipitated with anti-IGF2BP3 antibody or with normal rabbit IgG and Dynabeads Protein G (Dynal, Oslo, Norway) for 2 h at 4ºC. Beads were pelleted on a magnetic rack (Dynal). The immunoprecipitation products were treated with proteinase K, extracted with phenol-chloroform, and precipitated with ethanol. Purified RNAs were subsequently treated with DNase I (Promega, Madison, WI) and extracted using the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Finaly, RNAs were fragmented and purified using an Illumina TruSeq RNA Sample Prep Kit (San Diego, CA) according to the manufacturer’s instructions.
seq protocol: The IGF2BP3-associated mRNAs were identified using a next generation sequencer, Illumina HiSeq 2000 (Hokkaido System Science, Sapporo, Japan).

tag: antibody

value: control IgG

value: pancreatic cancer


title: Immunoprecipitated mRNAs with anti-IGF2BP3 antibody

description: library strategy: RIP-Seq

value: Anti-IGF2BP3 antibody


title: HUES9__4h__rep0

value: 4 hours since actD treatment


title: HUES9__2h__rep2

value: 2 hours since actD treatment


title: HUES9__2h__rep0


title: HUES9__2h__rep1


title: Smartseq.sc.r25ss72

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

description: FACS-isolated T-cell from mouse lymphocytes, lysed before preparation using SMART-seq 2

data_processing:
basecalls performed and fastq files generated on Miseq machine
bowtie alignment with -m 1 and output to .map with --chunkmbs 200
Genome_build: mouse mm10 unique isoforms
Supplementary_files_format_and_content: .map aligned files (bowtie)

source_name: T-Cell (FACS isolation)

extract_protocol:
Murine lymphocytes were isolated from B6CBF1 mouse spleen by homogenisation through a cell strainer in DMEM-10 media, followed by centrifugation through Lympholyte Ficoll (Cedarlane). Total RNA was extracted from the lymphocyte suspension using 1 mL Trizol (Ambion) and isolated with 500 μL chloroform before being ethanol precipitated.
First strand synthesis was performed in two separate reactions using the SMART cDNA synthesis kit (Takara Clontech), with different temperatures either 25C or 42C but otherwise following the manufacturers’ instructions. Libraries were then prepared for sequencing using Nextera XT kits and instructions. Smart-seq 2 and Quartz-seq protocols were also followed for some samples
Quartz-seq, SMART-seq and Smart-seq 2 (where indicated), followed by nextera and miseq preparations

treatment_protocol: First and Second strand synthesis temperature variations

value: T-Cell

tag: first strand synthesis temperature

tag: second strand synthesis temperature

tag: reverse transcription protocol

value: Smart-seq 2


title: Smartseq.sc.r25ss42


title: Smartseq.noPCR.f.ng.r42ss72

description: Poly(A) + RNA isolated from lymphocytes and prepared for sequencing using SMART-seq without a PCR after second strand synthesis

source_name: Mouse Lymphocyte

value: Lymphocyte

value: Smart-seq


title: HUES9__0.5h__rep2

value: 0.5 hours since actD treatment


title: Smartseq.noPCR.e.ng.r42ss72


title: Smartseq.noPCR.d.ng.r42ss72


title: HUES9__0.5h__rep1


title: HUES9__0.5h__rep0


title: Smartseq.sc.r42ss72


title: Smartseq.sc.r42ss42


title: Smartseq.noPCR.b.ng.r42ss72


title: HUES9__0.0h__rep1

value: control


title: Smartseq.noPCR.c.ng.r42ss72


title: HUES9__0.0h__rep2

value: 0 hours since actD treatment


title: HUES9__0.0h__rep0


title: Smartseq.d.pg.r42ss72

description: 10 pg Total RNA Prepared for sequencing using SMART-seq 2

source_name: Mouse Liver (Clontech)

value: Liver


title: Smartseq.noPCR.a.ng.r42ss72

description: Poly(A) + RNA isolated from lymphocytes and prepared for sequencing using SMART-seq with a PCR after second strand synthesis


title: HUES9__4h__rep1


title: Smartseq.c.ng.r42ss72

value: Smart-seq + PCR


title: Smartseq.b.pg.r42ss72


title: Smartseq.c.pg.r42ss72


title: SOX4_1DPT_Input

data_processing:
Genome_build: GRCh37/hg19
Reads were aligned to the human reference sequence GRCh37/hg19 with the Bowtie algorithm (version 1.0.0). Peak calling, peak‑gene annotation, motif discovery (parameter: 200 nucleotide window from peak center), and generation of heatmap matrices were performed using HOMER (version 4.7). Gene ontology classification was performed using HOMER and Genomic Regions Enrichment of Annotations Tool (version 2.0.2). The UCSC Genome Browser was used to visualize tag densities and multi-experiment datasets.
Supplementary_files_format_and_content: UCSC.bedGraph and peak files (.txt) were generated using HOMER (version 4.7).  The "merged" bedGraph and peak files represent multiple replicates that were combined to obtain a single bedGraph and peak file for each condition.

extract_protocol:
(Histone 3 lysine 27 acetylation) MRC-5 fibroblasts were cultured, transduced with NEUROG2-encoding lentivirus, and treated with neuron induction medium or neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin for 2 days. Approximately 1×10^7 cells were treated with Accutase cell detachment solution (Innovative Cell Technologies) for 3 minutes and collected in ice-cold PBS by centrifugation (525 × g, 5 minutes, 4°C). Cells were resuspended by repeated gentle pipetting in 4 ml ice-cold resuspension buffer (PBS containing 25 mM HEPES (pH 7.0) and 5 mM EDTA). GFP expressing viable cells were isolated using fluorescence-based sorting on a MoFlo platform (Beckman Coulter). Approximately 500,000 cells were collected by centrifugation (525 × g, 5 minutes, 4°C) then washed with 1 ml ice-cold PBS for chromatin digestion (Gilfillan et al., 2012). Cells were resuspended in 95 μl Micrococcal Nuclease digestion buffer (New England Biolabs, B0247S) supplemented with 0.01 μg BSA (New England Biolabs, B9001S), 0.2% (v/v) Triton X 100, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail. Resuspended cells were treated with 100 gel units Micrococcal Nuclease (New England Biolabs, M0247S) at 37°C for 5 minutes. Cells were immediately transferred to ice, treated with 10 μl ice-cold quench buffer (100 mM HEPES (pH 8.0) and 55 mM EDTA), and sonicated in a 1.5 ml TPX microtube for 60 seconds (power setting: high) using a Bioruptor equipped with a 4°C refrigerated water bath. Chromatin was diluted with 110 μl ice-cold immunoprecipitation buffer (50 mM HEPES (pH 8.0), 40 mM NaCl, 5 mM EDTA (pH 8.0), 0.2% (v/v) Triton X-100, 0.2% (w/v) SDS, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail), cell debris removed by centrifugation (21,130 × g, 10 minutes, 4°C), and 100 μl of supernatant transferred into two 0.2 ml microtubes (VWR, 732-0547). Chromatin was incubated with 1 μg rabbit polyclonal histone H3 acetyl K27 (Abcam, ab4729) antibody for 18 hours at 4°C with gentle nutation. The remaining 20 μl of supernatant was stored at  20°C as input. The following day, 20 μl Magnetic Protein G Dynabeads were washed three times with 200 μl ice-cold PBS containing 0.2% (v/v) Tween 20 on a MagneSphere separation stand at 4°C. The wash solution was removed and the beads were resuspended in 10 μl immunoprecipitation buffer then added to immunopreciptation samples for 2 hours at 4°C with gentle nutation. The bead complexes were magnetically isolated, twice washed by resuspension in 150 μl ice-cold immunoprecipitation buffer for 2 minutes, twice washed by resuspension in 150 μl ice-cold wash buffer (100 mM Tris-HCl (pH 9.0), 500 mM LiCl, 1% (v/v) IGEPAL CA-630, 1% (w/v) deoxycholic acid, and 1% (v/v) cOmplete EDTA free Protease Inhibitor Cocktail) for 1 minute, and finally resuspended in 150 μl ice-cold high salt wash buffer (wash buffer containing 150 mM NaCl) for transfer to a 1.5 ml microtube on ice followed by bead collection. Chromatin was eluted from collected beads in 50 μl elution buffer (1% (w/v) SDS and 50 mM NaHCO3) by two sequential additions of 25 µl elution buffer for 30 minutes at 27°C with vigorous agitation. Beads were magnetically collected and eluted chromatin was transferred to a sterile 1.5 ml microtube. Input chromatin was thawed on ice and treated with 50 μl elution buffer for 30 minutes at 27°C. Input and immunoprecipitated chromatin were sequentially treated with 10 μg RNase A for 15 minutes at 37°C and 80 μg Proteinase K for 3 hours at 55°C. Chromatin was purified with a QIAquick PCR purification kit and concentration was determined using a Qubit fluorometer and Qubit dsDNA HS assay kit as described above.
(Histone 3 lysine 27 methylation) MRC-5 fibroblasts were cultured, transduced with NEUROG2-encoding lentivirus, and treated with neuron induction medium or neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin for 2 days. Approximately 1×10^7 cells were treated with Accutase cell detachment solution (Innovative Cell Technologies) for 3 minutes and collected in ice-cold PBS by centrifugation (525 × g, 5 minutes, 4°C). Cells were resuspended by repeated gentle pipetting in 4 ml ice-cold resuspension buffer (PBS containing 25 mM HEPES (pH 7.0) and 5 mM EDTA). GFP expressing viable cells were isolated using fluorescence-based sorting on a MoFlo platform (Beckman Coulter). Approximately 500,000 cells were collected by centrifugation (525 × g, 5 minutes, 4°C) then washed with 1 ml ice-cold PBS for chromatin digestion (Gilfillan et al., 2012). Cells were resuspended in 95 μl Micrococcal Nuclease digestion buffer (New England Biolabs, B0247S) supplemented with 0.01 μg BSA (New England Biolabs, B9001S), 0.2% (v/v) Triton X 100, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail. Resuspended cells were treated with 100 gel units Micrococcal Nuclease (New England Biolabs, M0247S) at 37°C for 5 minutes. Cells were immediately transferred to ice, treated with 10 μl ice-cold quench buffer (100 mM HEPES (pH 8.0) and 55 mM EDTA), and sonicated in a 1.5 ml TPX microtube for 60 seconds (power setting: high) using a Bioruptor equipped with a 4°C refrigerated water bath. Chromatin was diluted with 110 μl ice-cold immunoprecipitation buffer (50 mM HEPES (pH 8.0), 40 mM NaCl, 5 mM EDTA (pH 8.0), 0.2% (v/v) Triton X-100, 0.2% (w/v) SDS, and 1% (v/v) cOmplete EDTA-free Protease Inhibitor Cocktail), cell debris removed by centrifugation (21,130 × g, 10 minutes, 4°C), and 100 μl of supernatant transferred into two 0.2 ml microtubes (VWR, 732-0547). Chromatin was incubated with 1 μg mouse monoclonal histone H3 tri-methyl K27 (Abcam, ab6002) antibody for 18 hours at 4°C with gentle nutation. The remaining 20 μl of supernatant was stored at  20°C as input. The following day, 20 μl Magnetic Protein G Dynabeads were washed three times with 200 μl ice-cold PBS containing 0.2% (v/v) Tween 20 on a MagneSphere separation stand at 4°C. The wash solution was removed and the beads were resuspended in 10 μl immunoprecipitation buffer then added to immunopreciptation samples for 2 hours at 4°C with gentle nutation. The bead complexes were magnetically isolated, twice washed by resuspension in 150 μl ice-cold immunoprecipitation buffer for 2 minutes, twice washed by resuspension in 150 μl ice-cold wash buffer (100 mM Tris-HCl (pH 9.0), 500 mM LiCl, 1% (v/v) IGEPAL CA-630, 1% (w/v) deoxycholic acid, and 1% (v/v) cOmplete EDTA free Protease Inhibitor Cocktail) for 1 minute, and finally resuspended in 150 μl ice-cold high salt wash buffer (wash buffer containing 150 mM NaCl) for transfer to a 1.5 ml microtube on ice followed by bead collection. Chromatin was eluted from collected beads in 50 μl elution buffer (1% (w/v) SDS and 50 mM NaHCO3) by two sequential additions of 25 µl elution buffer for 30 minutes at 27°C with vigorous agitation. Beads were magnetically collected and eluted chromatin was transferred to a sterile 1.5 ml microtube. Input chromatin was thawed on ice and treated with 50 μl elution buffer for 30 minutes at 27°C. Input and immunoprecipitated chromatin were sequentially treated with 10 μg RNase A for 15 minutes at 37°C and 80 μg Proteinase K for 3 hours at 55°C. Chromatin was purified with a QIAquick PCR purification kit and concentration was determined using a Qubit fluorometer and Qubit dsDNA HS assay kit as described above.
(NEUROG2) MRC-5 fibroblasts were cultured, transduced with NEUROG2+HA-SOX4-encoding lentivirus, and treated with neuron induction medium or neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin along the above described time course. Approximately 1×10^7 fibroblasts were treated with 16% (w/v) methanol-free formaldehyde (Thermo Scientific, 28908) at a final concentration of 1% (v/v) for 8 minutes at room temperature with gentle rotation following 24 hours in neuron induction medium. Cr

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.8×10^6 cells in a 10 cm polystyrene dish. Fibroblasts were transduced with NEUROG2+HA-SOX4-encoding lentivirus 24 hours after plating. The optimal lentivirus titer was empirically determined (4-fold dilution for 10 ml-capacity 10 cm dishes) and consistently yielded ≥90% TUBB3-positive and MAP2-positive neurons. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) supplemented with 10 μM forskolin (Sigma-Aldrich, F6886) and 1 μM dorsomorphin (Millipore, 171260) 48 hours post infection.

value: MRC-5 (ATCC, CCL-171)

tag: transduction (with factor)

value: NEUROG2, SOX4

tag: treatment (supplemented with medium and small molecules)

value: Neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin

tag: time (immunoprecipitation performed days post treatment with small molecules)

value: 1 DPT


title: SOX4_1DPT_IP2

value: Rabbit anti-HA polyclonal antibody (Abcam, AB9110)


title: IP2_NEUROG2_NFD_2DPT

value: 2 DPT


title: SOX4_1DPT_IP1


title: Smartseq.a.pg.r42ss72


title: Smartseq.a.ng.r42ss72


title: IP1_NEUROG2_NFD_1DPT


title: Smartseq.b.ng.r42ss72


title: Quartzseq.d.r42ss72

description: Poly(A) + RNA isolated from lymphocytes and prepared for sequencing using Quartz-seq

value: Quartz-seq


title: Quartzseq.c.r42ss72


title: IP2_NEUROG2_NFD_0.5DPT

value: 0.5 DPT


title: Quartzseq.b.r42ss72


title: IP1_NEUROG2_NFD_0.5DPT


title: Quartzseq.a.r42ss72


title: Smartseq.noPCR.e.ng.r42ss42


title: IP2_NEUROG2_N_2DPT

value: Neuron induction medium


title: IP1_NEUROG2_N_2DPT


title: Smartseq.noPCR.f.ng.r42ss42


title: Smartseq.noPCR.d.ng.r42ss42


title: IP2_NEUROG2_N_0.5DPT


title: IP2_NEUROG2_N_1DPT


title: Smartseq.noPCR.c.ng.r42ss42


title: IP1_NEUROG2_N_1DPT


title: SOX4_1DPT_IP3


title: Smartseq.noPCR.b.ng.r42ss42


title: Input_NEUROG2_NFD_2DPT


title: IP2_NEUROG2_NFD_1DPT


title: IP1_NEUROG2_NFD_2DPT


title: Quartzseq.e.r42ss72


title: Smartseq.c.ng.r42ss42


title: Smartseq.b.pg.r42ss42

value: Smart-seq 2


title: Smartseq.b.ng.r42ss42

value: Lymphocyte


title: IP1_NEUROG2_N_0.5DPT


title: Input_NEUROG2_NFD_1DPT


title: Smartseq.a.pg.r42ss42


title: Smartseq.noPCR.a.ng.r42ss42

value: Smart-seq


title: Input_NEUROG2_NFD_0.5DPT


title: Smartseq.a.ng.r42ss42


title: Input_NEUROG2_N_1DPT


title: Input_NEUROG2_N_0.5DPT


title: Input_NEUROG2_N_2DPT


title: IP2_H3K27ME3_NFD_1DPT

value: Mouse monoclonal histone 3 lysine 27 tri-methylation (Abcam, ab6002)


title: Quartzseq.e.r42ss42


title: Quartzseq.d.r42ss42


title: IP1_H3K27ME3_NFD_1DPT


title: Quartzseq.b.r42ss42


title: IP2_H3K27ME3_N_1DPT


title: IP1_H3K27ME3_N_1DPT


title: Quartzseq.c.r42ss42


title: Quartzseq.a.r42ss42


title: IP1_H3K27ME3_MRC5_1DPT

value: Dulbecco’s modified eagle medium supplemented with 15% (v/v) fetal bovine serum


title: Smartseq.noPCR.d.ng.r25ss72


title: Smartseq.noPCR.c.ng.r25ss72


title: IP2_H3K27AC_NFD_1DPT

value: Rabbit polyclonal histone 3 lysine 27 acetylation (Abcam, ab4729)


title: IP1_H3K27AC_NFD_1DPT


title: Smartseq.c.ng.r25ss72


title: IP2_H3K27AC_N_1DPT


title: IP2_H3K27AC_MRC5_1DPT


title: IP1_H3K27AC_N_1DPT


title: Smartseq.noPCR.f.ng.r25ss72


title: Smartseq.b.ng.r25ss72


title: Input_H3K27_N_1DPT


title: Quartzseq.d.r25ss72


title: RNA2_MRC5_NFD_2DPT

data_processing:
Genome_build: GRCh37/hg19
Reads were aligned to the human reference sequence GRCh37/hg19 with the TopHat (version 1.4.1) algorithm and transcript assembly performed with Cufflinks (version 2.1.0). Expression levels of RefSeq-annotated genes were calculated in units of fragments per kilobase of exon per million mapped fragments (FPKM) and differential expression analysis was performed with Cuffdiff (version 2.1.0). Genes were defined as significant if the following three criteria were satisfied: Student’s t-test p value ≥0.05, at least 2-fold gene expression change relative to the GFP-transduced control, and the triplicate average of ln(FPKM) ≥1 in either the experimental condition or fibroblast control. Gene ontology analysis was performed using the DAVID Functional Annotation Tool (version 6.7).
Supplementary_files_format_and_content: Condition_dependent_analysis.xlsx [FPKM and differential expression file generated using Cuffdiff (version 2.1.0)].

extract_protocol:
RNA isolation was performed 0.5, 1, and 2 DPT using TRIzol (Life Technologies, 15596-018) followed by chloroform extraction and column-based purification (Zymo Research, R1016). DPT (days post FD treatment) represents an arbitrary unit of time. All fibroblasts cultures were initially seeded and transduced at identical times while only a subset were exposed to small molecules. The isolation of RNA is described relative to the FD exposure event for all cultures to provide a clear timeline.
Libraries were synthesized from 4 μg purified RNA using a TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, RS‑122‑2201).
Single end 50-base length sequencing reads were generated on an Illumina HiSeq 2500 System.

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.3×10^6 cells in a 6 cm polystyrene dish. Fibroblasts were transduced with HA-NEUROG2-encoding lentivirus 24 hours after plating. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) supplemented with 10 μM forskolin (Sigma-Aldrich, F6886) and 1 μM dorsomorphin (Millipore, 171260) 48 hours post infection.

tag: time (rna isolation performed days post treatment with small molecules)


title: RNA1_MRC5_NFD_2DPT


title: Smartseq.a.pg.r25ss72

value: Liver


title: Input_H3K27_NFD_1DPT


title: Input_H3K27_MRC5_1DPT


title: Smartseq.b.pg.r25ss72


title: IP2_H3K27ME3_MRC5_1DPT


title: Quartzseq.c.r25ss72


title: Smartseq.noPCR.e.ng.r25ss72


title: RNA3_MRC5_NFD_2DPT


title: Quartzseq.b.r25ss72


title: Smartseq.noPCR.a.ng.r25ss72


title: Smartseq.noPCR.b.ng.r25ss72


title: RNA3_MRC5_N_2DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.3×10^6 cells in a 6 cm polystyrene dish. Fibroblasts were transduced with HA-NEUROG2-encoding lentivirus 24 hours after plating. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) 48 hours post infection.


title: Quartzseq.a.r25ss72


title: RNA1_MRC5_N_2DPT


title: RNA3_MRC5_FD_2DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.3×10^6 cells in a 6 cm polystyrene dish. Fibroblasts were transduced with GFP-encoding lentivirus 24 hours after plating. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) supplemented with 10 μM forskolin (Sigma-Aldrich, F6886) and 1 μM dorsomorphin (Millipore, 171260) 48 hours post infection.

value: GFP


title: IP1_H3K27AC_MRC5_1DPT

value: MRC-5 (ATCC, CCL-171)


title: Smartseq.noPCR.e.ng.r25ss42


title: Smartseq.noPCR.f.ng.r25ss42


title: RNA2_MRC5_FD_2DPT


title: RNA1_MRC5_FD_2DPT


title: Smartseq.a.ng.r25ss72

value: Smart-seq + PCR


title: Quartzseq.e.r25ss72


title: Smartseq.noPCR.d.ng.r25ss42


title: RNA3_MRC5_GFP_2DPT

treatment_protocol: MRC-5 fibroblasts were seeded at a density of 0.3×10^6 cells in a 6 cm polystyrene dish. Fibroblasts were transduced with GFP-encoding lentivirus 24 hours after plating. Transduced-fibroblast cultures were treated with fresh medium 24 hours post infection. Cultures were transitioned to neuron induction medium (DMEM, Ham’s F12 nutrient mixture (GE Healthcare, SH30026.02), neurobasal medium (Life Technologies, 21103-049), N-2 supplement (Life Technologies, 17502‑048), B-27 supplement (Life Technologies, 17504-044), and penicillin‑streptomycin at 1 : 1 : 0.5 : 0.02 : 0.01 : 0.025) 48 hours post infection.


title: Smartseq.noPCR.c.ng.r25ss42


title: RNA2_MRC5_GFP_2DPT


title: RNA2_MRC5_N_2DPT


title: RNA1_MRC5_GFP_2DPT


title: Smartseq.noPCR.a.ng.r25ss42


title: RNA3_MRC5_NFD_1DPT

value: Neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin


title: Smartseq.d.pg.r25ss42


title: Smartseq.c.pg.r25ss42


title: RNA1_MRC5_NFD_1DPT

value: 1 DPT


title: RNA2_MRC5_NFD_1DPT


title: Smartseq.c.ng.r25ss42


title: TAPRESTkd_N4_RNA-seq

first: Jenny

last: Hsieh

address: 6001 Forest Park Road, NA6.514AA

institute: UT Southwestern Medical Center

description:
RiboZero cleaned, total RNA
Cuffdiff_TAPCtrlvsTAPRESTkd.xls

data_processing:
Reads were mapped on rn4 genome using Tophat2 and differential gene expression was determined by Cufflink and Cuffdiff.
Genome_build: rn4 (RGSC_v3.4)
Supplementary_files_format_and_content: excel file of Cuffdiff output to test differentially expressed genes for two or four replicates of each treatment

organism: Rattus norvegicus

source_name: HCN cells in TAP or proliferative growth condition

growth_protocol: HCN cells were grown in quiescence (FGF2+BMP4+) or proliferation (FGF+ only) conditions on adherent plates as monolayer (typically 2–3 × 106 cells per 10cm plate) in DMEM:F12 (Omega Scientific Inc.) media supplemented with N2, glutamate and PSF.

extract_protocol:
RNA was extracted using miRNAeasy kit Qiagen 217004. Ribosomal RNA was removed using RiboZero kit Epicenter. Libraries were prepared using standard Illumina protocol and sequenced on Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols, and sequenced on Illumina platform, Illumina HiSeq 2500

treatment_protocol: HCN cells were either non-electroporated or electroporated with empty vector or REST knock-down shRNA vector

value: hippocampal neural stem (HCN) cells derived from the adult rat brain

tag: passages

value: multiple

tag: growth condition

value: TAP

tag: treatment

value: electroporated with Restkd vector


title: TAPRESTkd_N3_RNA-seq


title: RNA2_MRC5_N_1DPT

value: Neuron induction medium


title: Smartseq.b.pg.r25ss42

tag: tissue

value: Smart-seq 2


title: RNA3_MRC5_N_1DPT

tag: cell line


title: TAPCt_N2_RNA-seq

value: electroporated with empty vector


title: TAPRESTkd_N2_RNA-seq


title: TAPCt_N1_RNA-seq


title: Smartseq.b.ng.r25ss42

value: Lymphocyte


title: TAPRESTkd_N1_RNA-seq


title: iQNPRESTkd_N3_RNA-seq

description:
RiboZero cleaned, total RNA
Cuffdiff_iQNPCtrlvsiQNPRESTkd.xls

source_name: HCN cells in iQNP or quiescent growth condition

value: iQNP


title: RNA1_MRC5_N_1DPT


title: iQNPRESTkd_N4_RNA-seq


title: iQNPRESTkd_N2_RNA-seq


title: Smartseq.a.pg.r25ss42


title: RNA3_MRC5_FD_1DPT


title: Smartseq.noPCR.b.ng.r25ss42

value: Smart-seq


title: iQNPRESTkd_N1_RNA-seq


title: RNA2_MRC5_FD_1DPT


title: iQNPCt_N1_RNA-seq


title: iQNPCt_N2_RNA-seq


title: Quartzseq.e.r25ss42

value: Quartz-seq


title: Quartzseq.d.r25ss42


title: RNA1_MRC5_FD_1DPT


title: RNA3_MRC5_GFP_1DPT

value: Dulbecco’s modified eagle medium supplemented with 15% (v/v) fetal bovine serum


title: Quartzseq.c.r25ss42


title: REST_antibody2_TAP_ChIPSeq

description: REST_antibody1antibody2_TAP_ChIPSeq_HomerPk.txt

data_processing:
ChIP-seq reads were aligned to the rn4 genome assembly using Bowtie2 with default settings
Data were filtered using the following specifications…
HOMER peak calling and merge peak function was used for peak calling, using default settings
Genome_build: rn4 (RGSC_v3.4)
Supplementary_files_format_and_content: Output from HOMER peak calling and merge peak function is shown

extract_protocol:
Covaris ChIP protocol was followed https://ethanomics.files.wordpress.com/2012/01/chip_covaris4.pdf
Libraries were prepared according to Illumina's instructions and sequenced on Illumina platform, Illumina HiSeq 2500

tag: chip antibody

value: anti-REST (Hsieh lab homemade antibody)


title: Input DNA_iQNP_ChIPSeq

description: REST_antibody1antibody2_iQNP_ChIPSeq_HomerPk.txt


title: RNA2_MRC5_GFP_1DPT

value: MRC-5 (ATCC, CCL-171)

value: GFP


title: REST_antibody1_iQNP_ChIPSeq

value: anti-REST (Millipore, 17-641)


title: REST_antibody2_iQNP_ChIPSeq


title: Quartzseq.b.r25ss42


title: RNA3_MRC5_NFD_0.5DPT

value: Neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin

value: 0.5 DPT


title: Yorkshire_2

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
Genomic DNA from skin fibroblast  was extracted, and sequenced by WGBS technology using Illumina HiSeq2000 sequencer.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% ’N’s or over 50% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the reference genome using BSMAP software.
The uniquely aligned reads were used for methylation analysis.
Genome_build: canFam2
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads
Supplementary_files_format_and_content: Cout file format:  (1)Chromosome ID   (2)Cytosine position  (3)+/- Watson/Crick chain  (4)Type (CG/CHH/CHG)  (5)Base pattern  (6)Copy number  (7)Methy reads num  (8)Nonmethy reads num  (9)Expected value

organism: Canis lupus familiaris

extract_protocol:
DNA was isolated using a DNA QIAGEN QIAamp DNA Mini Kit  following the manufacturer’s protocols.
Genomic DNA was sonicated to 200-300 bp using the Covaris S2 system and then the fragmented DNA was end-repaired using a combination of T4 Polynucleotide Kinase and Klenow polymerase .The blunt, phosphorylated ends were treated with Klenow fragment (3’-5’ exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's methylated adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation , the DNA was bisulphite treated using the EZ DNA Methylation-Gold Kit (ZYMO),and then PCR amplified using JumpStart Taq DNA Polymerase (Sigama)

tag: group

value: Control

value: skin fibroblast


title: RNA1_MRC5_GFP_1DPT

value: 1 DPT


title: Yorkshire_1


title: CPF100

value: Clone


title: Quartzseq.a.r25ss42


title: GSF102

value: Reclone


title: Smartseq.a.ng.r25ss42

value: Smart-seq + PCR


title: Trakr_origin

value: Origin


title: RNA2_MRC5_NFD_0.5DPT


title: Input DNA_TAP_ChIPSeq

value: hippocampal neural stem (HCN) cells derived from the adult rat brain

value: multiple

value: TAP


title: RNA1_MRC5_NFD_0.5DPT


title: RNA2_MRC5_N_0.5DPT

value: Neuron induction medium


title: Astro_origin


title: RNA1_MRC5_N_0.5DPT


title: RNA3_MRC5_N_0.5DPT


title: RNA1_MRC5_FD_0.5DPT


title: RNA2_MRC5_FD_0.5DPT


title: RNA1_MRC5_GFP_0.5DPT

value: Dulbecco’s modified eagle medium supplemented with 15% (v/v) fetal bovine serum


title: RNA2_MRC5_GFP_0.5DPT

value: MRC-5 (ATCC, CCL-171)


title: REST_antibody1_TAP_ChIPSeq


title: pancreatic_cancer_1

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

institute: Kunming Institute of Zoology

description:
pancreatic cancer
MPC_1

data_processing:
Basecalls performed using CASAVA version 1.8
Data were filtered using GSQCToolkitv2.3.3 with parameters –pe -cutOffReadLen4HQ 70 –cutOffQualScore 20 N 5.
RNA-seq reads were aligned to the GRCm38.p4 genome assembly using Tophat-2.1.0 with read-mismatches=2.
The fragments per kilobase of transcript per million fragments (FPKM) of the genes were calculated using express cufflinks2.2.1, --max-multiread-fraction 0.75, Cuffnorm all samples from different stages, –library-norm-method is genometric. Then raw data was transform into logarithm, log2(FPKM +1).
Genome_build: GRCm38.p4

source_name: pancreas

extract_protocol: The RNA sequencing libraries were constructed using the Illumina mRNA-Seq Prep Kit, and they were sequenced on the Illumina HiSeq 2000 platform in paired-end reads with 150 bp length

tag: cell type

value: Tissue

tag: strain

tag: genotype/variation


title: 9_week_3

value: 9 week


title: 9_week_2


title: 9_week_1


title: 6_week_3

value: 6 week


title: GSF74


title: 6_week_2


title: 6_week_1


title: 3_week_3

value: 3 week


title: QK5-CLIP_PM29

city: Houston

first: Jian

last: Hu

address: 1881 East Rd

department: Department of Cancer Biology, Division of Basic Sciences

institute: The University of Texas MD Anderson Cancer Center

description: RNA isolated by PAR-CLIP

data_processing:
Sequenced reads were mapped to the mm10 genome using tophat2/2.0.8.
A single-linkage clustering of the sequence reads was performed for reads with at least 1bp overlap in genomic mappings. High confidence clusters are identified and annotated according to Hafner et al. Cell. 2010 Apr 2;141(1):129-41.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include annotated CLIP peaks  in each sample

source_name: QPP glioblastoma stem cells (GSCs)

extract_protocol:
RNAs  extracted following the PAR-CLIP protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: glioblastoma stem cells

tag: genotype

value: Pten-/- p53-/- QKI-/- with QKI-5 overexpresion

tag: affinity purification

value: anti-HA immunoprecipitation


title: New_born_3

value: New born


title: New_born_1


title: New_born_2


title: 3_week_1


title: QK6-CLIP_PM29

description: RNA isolated by PAR-CLIP

value: Pten-/- p53-/- QKI-/- with QKI-6 overexpresion


title: RNA3_MRC5_FD_0.5DPT

value: GFP

value: Neuron induction medium supplemented with 10 μM forskolin and 1 μM dorsomorphin

value: 0.5 DPT


title: RNA3_MRC5_GFP_0.5DPT


title: pancreatic_cancer_3

description:
pancreatic cancer
MPC_3


title: pancreatic_cancer_2

description:
pancreatic cancer
MPC_2


title: TKO-tumor_RNA25_14370

description: processed data files: TKO-tumor_RNA25_gene_FPKM.txt.gz and TKO-tumor_RNA25_transcript_FPKM.txt.gz

data_processing:
Sequenced reads were mapped to the mm10 genome using tophat2/2.0.8. Transcription annotation version is GENCODE vM8.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated at both gene and transcript level using cufflinks/2.2.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: QPP mouse glioblastoma

growth_protocol: Cells were grown in neural stem cell medium with EGF/FGF

extract_protocol:
Total RNAs were extracted with Rnasey kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either EtOH or 4OHT. Mice were injected with tamoxifen at P8-10.

value: glioblastoma

value: tamoxifen


title: TKO-tumor_RNA25_14448


title: TKO-tumor_RNA25_14447


title: TKO-tumor_RNA25_14235


title: TKO-tumor_RNA25_14257


title: TKO-tumor_RNA25_14368


title: TKO-tumor_RNA25_14184


title: TKO-tumor_RNA25_14197


title: TKO-tumor_RNA25_14211


title: TKO-tumor_RNA25_14242


title: TKO-tumor_RNA25_14109


title: 3_week_2


title: TKO-tumor_RNA25_12181


title: TKO-tumor_RNA25_13147


title: TKO-tumor_RNA25_13141


title: TKO-tumor_RNA25_13143


title: TKO-tumor_RNA25_12176


title: TKO-DKO-Nu95_QPP8_KO

description:
isolate from postnatal day one pup
processed data files: TKO-DKO-Nu95_gene_FPKM.txt.gz and TKO-DKO-Nu95_transcript_FPKM.txt.gz

source_name: pre-malignant neural stem cells (PM-NSCs)

value: neural stem cells


title: TKO-DKO-Nu95_QPP7_KO


title: TKO-DKO-Nu95_QPP1_KO


title: TKO-DKO-Nu95_PP3_WT


title: TKO-DKO-Nu95_PP9_WT


title: TKO-DKO-Nu95_QPP12_KO


title: TKO-DKO-Nu95_PP10_WT


title: TKO-DKO-Nu95_PP11_WT


title: QK-NSC-KO_QW9-40HT_WT

description:
isolate from postnatal day one pup
processed data files: QK-NSC-KO_gene_FPKM.txt.gz and QK-NSC-KO_transcript_FPKM.txt.gz

source_name: neural stem cells (NSCs)

value: wild type


title: QK-NSC-KO_QW5_WT

value: EtOH


title: QK-NSC-KO_QW5-40HT_KO

value: QKI-/-


title: QK-NSC-KO_QW3_WT


title: QK-NSC-KO_QW3-40HT_KO


title: QK-NSC-KO_QW2-40HT_WT


title: QK-NSC-KO_QW2_WT


title: QK-NSC-KO_QW9_WT


title: total RNA-seq from lower leg skin (ENCLB253MPS)

status: Public on Nov 08 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR991HIR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's skin of the lower leg tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR991HIR
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB253MPS
size range: >200
spikeins used: /references/ENCSR156CIL/

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens lower leg skin tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/34f4e4ff-b9cc-445c-ad25-a68d315caf29/@@download/attachment/296602.pdf

value: lower leg skin

value: tissue

tag: description

value: Skin of the lower leg aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

tag: biosample encode accession

tag: age

value: 53 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS432ZSQ at ENCODE; https://www.encodeproject.org/ENCBS432ZSQ/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: RAMPAGE from ovary (ENCLB006TFZ)

description:
https://www.encodeproject.org/experiments/ENCSR983ICQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human female gonad tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR983ICQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR841ADZ
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB006TFZ
size range: >200

source_name: Homo sapiens ovary tissue female adult (53 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1a2f3fec-1a06-48fa-992c-79e09d31812b/@@download/attachment/296815.pdf

value: ovary

value: Ovary tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: ENCBS688BQS at ENCODE; https://www.encodeproject.org/ENCBS688BQS/


title: shRNA RNA-seq from K562 (ENCLB444JLX)

description:
https://www.encodeproject.org/experiments/ENCSR978CSQ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PKM2. (PKM2_BGKLV21-B)
experiment encode accession: ENCSR978CSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB444JLX
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting PKM

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b63b265c-230b-42eb-9a5d-235d4cea68af/@@download/attachment/L-PKM2_BGKLV21-42B.pdf

tag: antibody

value: PKM

tag: line

value: immortalized cell line

value: RNA-seq on K562 cells treated with an shRNA knockdown against PKM2. (PKM2_BGKLV21-42B)

tag: health state

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS628JQT at ENCODE; https://www.encodeproject.org/ENCBS628JQT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from HepG2 (ENCLB034DMC)

description:
https://www.encodeproject.org/experiments/ENCSR995JMS/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGHLV30)
experiment encode accession: ENCSR995JMS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB034DMC
size range: >200
spikeins used: /references/ENCSR449DXG/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting HNRNPM

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/13aab3c6-2e42-4bcb-9cf6-12e22d2e640e/@@download/attachment/L-HNRNPM_BGHLV30-41.pdf

value: HNRNPM

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGHLV30-41)

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS087QWF at ENCODE; https://www.encodeproject.org/ENCBS087QWF/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB288MWV)

description:
https://www.encodeproject.org/experiments/ENCSR995JMS/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGHLV30)
experiment encode accession: ENCSR995JMS
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR067GHD
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB288MWV
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2db7a8ae-5e9f-4ee2-b96d-b87589c5aacb/@@download/attachment/L-HNRNPM_BGHLV30-42.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against HNRNPM. (HNRNPM_BGHLV30-42)

value: ENCBS839SGI at ENCODE; https://www.encodeproject.org/ENCBS839SGI/


title: total RNA-seq from gastrocnemius medialis (ENCLB257CMY)

description:
https://www.encodeproject.org/experiments/ENCSR967JPI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's skeletal muscle tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR967JPI
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB257CMY
size range: >200
spikeins used: /references/ENCSR156CIL/

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ce69a696-cbdf-4585-865d-0292ee8a7c67/@@download/attachment/296167.pdf

value: gastrocnemius medialis

value: tissue

value: skeletal muscle tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS472LWI at ENCODE; https://www.encodeproject.org/ENCBS472LWI/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: shRNA RNA-seq from HepG2 (ENCLB573XYH)

description:
https://www.encodeproject.org/experiments/ENCSR968BBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV22B)
experiment encode accession: ENCSR968BBQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB573XYH
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens HepG2 immortalized cell line transiently expressing shRNA targeting Non-specific target control

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b35d9b01-25a3-425d-821c-93c0d19a7a78/@@download/attachment/L-NT_BGHLV22-1B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV22-1B)

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS961ZJH at ENCODE; https://www.encodeproject.org/ENCBS961ZJH/


title: shRNA RNA-seq from K562 (ENCLB822BJU)

description:
https://www.encodeproject.org/experiments/ENCSR978CSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against PKM2. (PKM2_BGKLV21-B)
experiment encode accession: ENCSR978CSQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR438MDN
encode release date: 2016-03-16
lab: Brenton Graveley, UConn
library encode accession: ENCLB822BJU
size range: >200
spikeins used: /references/ENCSR449DXG/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/b870011a-87b8-4b09-9e46-5b4d864af250/@@download/attachment/L-PKM2_BGKLV21-41B.pdf

value: PKM

value: RNA-seq on K562 cells treated with an shRNA knockdown against PKM2. (PKM2_BGKLV21-41B)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS061SQD at ENCODE; https://www.encodeproject.org/ENCBS061SQD/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: shRNA RNA-seq from HepG2 (ENCLB167SEG)

description:
https://www.encodeproject.org/experiments/ENCSR968BBQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV22B)
experiment encode accession: ENCSR968BBQ
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB167SEG
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/f5780545-7e91-4629-b9a8-d26327cd9c32/@@download/attachment/L-NT_BGHLV22-2B.pdf

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV22-2B)

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS455OVD at ENCODE; https://www.encodeproject.org/ENCBS455OVD/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: shRNA RNA-seq from HepG2 (ENCLB909ZOU)

description:
https://www.encodeproject.org/experiments/ENCSR960MSV/
***************
biological replicate number: 1
technical replicate number: 1
description: Control shRNA against no target in HepG2 cells followed by RNA-seq. (NT_BGHLV27B)
experiment encode accession: ENCSR960MSV
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Brenton Graveley, UConn
library encode accession: ENCLB909ZOU
size range: >200
spikeins used: /references/ENCSR358OMW/

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/2a070edf-6dea-4c10-b1fb-8264b149867a/@@download/attachment/L-NT_BGHLV27-1B.pdf

value: Control

value: immortalized cell line

value: RNA-seq on HepG2 cells treated with an shRNA knockdown against non-target. (NT_BGHLV27-1B)

value: 15 year

value: Brenton Graveley, UConn

value: ENCBS342VWN at ENCODE; https://www.encodeproject.org/ENCBS342VWN/


title: RAMPAGE from Peyer's patch (ENCLB881LYI)

description:
https://www.encodeproject.org/experiments/ENCSR954YVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human ileum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR954YVZ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR257NIR
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB881LYI
size range: >200

source_name: Homo sapiens Peyer's patch tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/917eeb97-299f-4a4c-99b7-81c9e751a6e3/@@download/attachment/296781.pdf

value: Peyer's patch

value: tissue

value: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS943XLR at ENCODE; https://www.encodeproject.org/ENCBS943XLR/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: shRNA RNA-seq from K562 (ENCLB498JUF)

description:
https://www.encodeproject.org/experiments/ENCSR945GUR/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with an shRNA knockdown against NAA15. (NAA15_BGKLV32)
experiment encode accession: ENCSR945GUR
assay title: shRNA RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR143COQ
encode release date: 2016-06-30
lab: Brenton Graveley, UConn
library encode accession: ENCLB498JUF
size range: >200
spikeins used: /references/ENCSR358OMW/

source_name: Homo sapiens K562 immortalized cell line transiently expressing shRNA targeting NAA15

extract_protocol:
extraction method: Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
general protocol: https://www.encodeproject.org/documents/ce67cb5a-32aa-43d2-9426-d9ee18f9e77f/@@download/attachment/L-NAA15_BGKLV32-41.pdf

value: RNA-seq on K562 cells treated with an shRNA knockdown against NAA15. (NAA15_BGKLV32-41)

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS171PLV at ENCODE; https://www.encodeproject.org/ENCBS171PLV/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004