title: Oscar consortium sample day 28, biological replicate C

city: West Lafayette

first: Stephen

middle: R

last: Lindemann

state: IN

address: 745 Agriculture Mall Drive

department: Food Sciences

institute: Purdue University

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D28_C RNA 09/09/13 JC/MB
28C
Processed data file: Oscar_summary_table.txt

data_processing:
The 50-base read sequences produced by the 5500XL SOLiD sequencer were mapped in color space using SOLiD LifeScope software version 2.5 using the default parameters against an artificial chromosome constructed by concatenating genomes of all isolated members and all contigs of all consortium members, each separated by ten ambiguous nucleotides to prevent edge effects that might otherwise disturb mapping near contig boundaries.
Reads were converted to RPKM for each bin (organism) after filtering out tRNA and other non-CDS reads using the total CDS counts for that organism as the base number.
Final reads for each CDS were cross referenced to the Locus Tag and annotations for each isolated organism (annotation version 0715).
Each sample is named for the collection date and the biological replicate.
Genome_build: PNNL_OSCAR_ref_metagenome_June_2015_GTF.gtf, PNNL_OSCAR_ref_metagenome_June_2015_FASTA.fasta
Supplementary_files_format_and_content: *txt: Tab-delimited gene rollup text files listing the gene counts and RPKMs for each sample.

organism: phototrophic enrichment culture UCC-O

source_name: Cell culture

growth_protocol: Sequentially-passaged enrichment cultures were inoculated at a 1:50 dilution into HLA medium (BG-11 medium supplemented with 400 mM MgSO4, 100 mM Na2SO4 and 25 mM KCl at pH 8.0) in T75 tissue culture flasks with vented caps (Costar, Corning, Inc., Corning, NY) under 35 mE m-2 s-1 irradiance from a fluorescent grow light (General Electric PL/AQ, Fairfield, CT). Cultures were incubated for 28 days and rehydrated weekly to maintain salinity, with triplicate biological replicates (parallel T-75 flasks) harvested and split for transcriptomic analysis at 7, 14, 21, and 28 days of cultivation.

extract_protocol:
RNA was extracted using Invitrogen TRIzol® Reagent (cat#15596018), followed by genomic DNA removal and cleaning using Qiagen RNase-Free DNase Set kit (cat#79254) and Qiagen Mini RNeasy™ kit (cat#74104). Agilent 2100 Bioanalyzer was used to assess the integrity of the RNA samples. Only RNA samples having RNA Integrity Number between 8-10 were used.
The Applied Biosystems SOLiD Total RNA-Seq kit (cat. #4445374) was used to generate the cDNA template library per manufacturer’s instructions. The SOLiD EZ Bead system was used to perform emulsion clonal bead amplification to generate bead templates for sequencing on the 5500XL SOLiD platform.

treatment_protocol: No experimental treatments.

tag: cell type

value: Uni-cyanobacteria consortium

value: day 28

tag: cell number per plate


title: Oscar consortium sample day 28, biological replicate B

status: Public on May 24 2017

type: SRA

country: USA

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D28_B RNA 09/09/13 JC/MB
28B
Processed data file: Oscar_summary_table.txt

library_source: transcriptomic

molecule: total RNA

tag: time point


title: Oscar consortium sample day 28, biological replicate A

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D28_A RNA 09/09/13 JC/MB
28A
Processed data file: Oscar_summary_table.txt


title: ath_circRNA without stress treatments

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

data_processing:
the NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
Sequence alignments were performed using tophat2 with BOWTIE2 (v2.0.5) (Langmead and Salzberg, 2012) for mapping to the reference genome (Arabidopsis_thaliana TAIR10.30 ENSEMBL).
The circRNAs were predicted using the find_circ program with the same parameters as described previously
Chimeric mapped reads were selected for circular (“back-spliced”) junctions if the sequence reads mapped to one chromosome on the same strand, while the two sequence segments mapped to the genomic region with reverse order. CircRNA abundance was predicted on the basis of circular junction read counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text file includes CircRNA_name, chr,start,end, circRNA_type, gene_id,  strand, Mean_junction, gene_length
Supplementary_files_format_and_content: CircRNA abundance

organism: Arabidopsis thaliana

source_name: ath circRNA without stress treatments

growth_protocol: Wild-type (WT) A. thaliana Columbia ecotype (Col-0) was cultivated at 23/18℃ under 16/8 light/dark cycle.

extract_protocol: Strand-specific RNA library was prepared according to Illumina's instructions.  Briefly,The rRNA-depleted RNAs was firstly fragmented into short sequences in fragmentation buffer at 94 °C for 15 min. Secondly, these fragments were used as templates for first-strand cDNA synthesis primed with random hexamers. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H, and DNA polymerase I, followed by AMPure XP beads purification. Thirdly, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. After that, the fragments are connected with adapters, then the second strand containing “U” is degraded using USER (uracil-specific excision reagent). Finally, suitable fragments were selected as templates for the PCR amplification after agarose gel electrophoresis. The quantification and qualification of the libraries were further assessed by using Agilent 2100 Bioanaylzer (Agilent Technologies, Palo Alto, CA) and Qubit® 2.0 Fluorometer (Invitrogen).

treatment_protocol: seedlings at stage 3.90 were exposed to the following stress environments: 300 mM/L mannitol (drought), 200 mM NaCl (salinity), and 38℃ (heat).

tag: tissue

value: whole plants


title: ath_circRNA Siliques

source_name: ath circRNA Siliques

value: siliques


title: luc7_seedlings_rep3

city: Cologne

first: Eva-Maria

last: Willing

address: Carl-von-Linne Weg 10

country: Germany

institute: MPIPZ

data_processing:
tophat (v2.0.10) was used for spliced alignments against A. thaliana reference genome (TAIR10)
cufflinks (version 2.2.1) was used to extract FPKM counts
Genome_build: TAIR10
Supplementary_files_format_and_content: text files, cufflinks output files

molecule: polyA RNA

source_name: 7 days old seedlings

growth_protocol: 7 days old seedlings growing on 1/2 MS medium with 0,8% phytoagar on continuous light conditions at 22°C.

extract_protocol:
Total RNA  was extracted with Direct-zol™ RNA MiniPrep Kit (Zymo Research) and 4 µg was used to isolate polyadenylated RNAs with NEBNext Oligo d(T)25 Magnetic Beads (E7490, Biolabs).
The libraries were done with ScriptSeq™ Plant Leaf kit (Epicentre) following the manufacturer's instruction. Single end sequencing was performed on an Illumina HiSeq2000.

tag: ecotype/genotype

value: triple mutant (luc7 a-2, b-1, rl-1)

tag: developmental stage

value: 7 days old seedlings


title: Oscar consortium sample day 21, biological replicate C

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D21_C RNA 09/02/13 JC/MB
21C
Processed data file: Oscar_summary_table.txt

value: day 21


title: F. tularensis treated with human erythrocyte, replicate 5

city: Huntington

first: Swanthana

last: Rekulapally

state: WV

address: 1 John Marshall Drive

department: Biomedical Sciences

institute: Marshall University

data_processing:
Demultiplexing of samples was performed using CASAVA 1.8.2 (Illumina).
Reads were aligned to the F. tularensis (subspecies holarctica LVS) genome using Bowtie2-2.2.5
Raw and normalized read counts, and differential expression analysis, were conducted using a DESeq2 pipeline
Genome_build: NC_007880.1
Supplementary_files_format_and_content: tab-delimited text files containing raw and normalized read counts were extracted from the DESeq2-generated R data files

organism: Francisella tularensis

growth_protocol: Frozen stock cultures of bacteria were streaked onto chocolate II agar plates and incubated at 37°C with 5% carbon dioxide for 1-3 days.  These bacteria were used to inoculate Chamberlain’s chemically defined medium and grown to stationary phase by an overnight incubation at 37°C with agitation.

extract_protocol:
Total RNA was extracted from bacterial cells using a Qiagen RNeasy kit
LVS RNA-Seq libraries were prepared from 1000 ng total RNA using an Epicentre ScriptSeq Complete Kit
Libraries were sequenced in a 2 x 50 base paired end strategy on an Illumina HiSeq1500 sequencer.

treatment_protocol: Human erythrocytes were isolated from buffy coats obtained from Pittsburgh Central Blood Bank.  The buffy coat or blood sample was then mixed with an equal volume of  phosphate-buffered saline (PBS; Cellgro) and separated by density gradient centrifugation using Ficoll (GE Heatlthcare Bio-sciences). Erythrocytes were suspended in complete M5A and aliquoted into a 96-well V-bottom microtiter dish (Nunc).  Bacteria from overnight broth cultures were suspended in complete M5A and incubated at 37°C for 20 minutes prior to infection.  Bacteria were then added to the erythrocytes and incubated together at 37°C with 5% carbon dioxide for 2-3 hours.

tag: strain

value: LVS


title: F. tularensis control treated, replicate 5


title: ath_circRNA flowers

source_name: ath circRNA flowers

value: flowers


title: F. tularensis control treated, replicate 4


title: Oscar consortium sample day 21, biological replicate B

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D21_B RNA 09/02/13 JC/MB
21B
Processed data file: Oscar_summary_table.txt


title: Oscar consortium sample day 21, biological replicate A

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D21_A RNA 09/02/13 JC/MB
21A
Processed data file: Oscar_summary_table.txt


title: F. tularensis treated with human erythrocyte, replicate 4


title: ath_circRNA stems

source_name: ath circRNA stems

value: stems


title: control (p45+/–) Tfh rep2

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample …

organism: Mus musculus

source_name: non-GC-Tfh cells

extract_protocol:
non-GC Tfh cells were sort-purified and total RNA was extracted using standard Qiagen RNase columns.
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: genotype

value: spleen

tag: cell phenotype

value: CD45.2+CD4+CXCR5+PD-1 negative


title: Oscar consortium sample day 14, biological replicate C

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D14_C RNA 08/26/13 JC/MB
14C
Processed data file: Oscar_summary_table.txt

value: day 14


title: Oscar consortium sample day 14, biological replicate B

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D14_B RNA 08/26/13 JC/MB
14B
Processed data file: Oscar_summary_table.txt


title: F. tularensis control treated, replicate 3


title: Oscar consortium sample day 14, biological replicate A

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D14_A RNA 08/26/13 JC/MB
14A
Processed data file: Oscar_summary_table.txt


title: ath_circRNA roots

source_name: ath circRNA roots

value: roots


title: F. tularensis control treated, replicate 2


title: Oscar consortium sample day 7, biological replicate C

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D07_C RNA 08/19/13 JC/MB
7C
Processed data file: Oscar_summary_table.txt

value: day 7


title: ath_circRNA 8.00

source_name: ath circRNA 8.00


title: ath_circRNA 6.50

source_name: ath circRNA 6.50


title: F. tularensis treated with human erythrocyte, replicate 2


title: ath_circRNA 3.90

source_name: ath circRNA 3.90


title: Oscar consortium sample day 7, biological replicate A

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D07_A RNA 08/19/13 JC/MB
7A
Processed data file: Oscar_summary_table.txt


title: Oscar consortium sample day 7, biological replicate B

description:
Unicyanobacterial consortium Oscar (UCC-O)
Succession series in which the change in species abundance and composition in a simplified natural community is monitored over time. Thus, time is the only variable.
mRNA
Osc_D07_B RNA 08/19/13 JC/MB
7B
Processed data file: Oscar_summary_table.txt


title: F. tularensis treated with human erythrocyte, replicate 1


title: ath_circRNA leaves

source_name: ath circRNA leaves

value: leaves


title: singles-K562-141106-92

status: Public on May 23 2017

city: Stanford

first: William

middle: J

last: Greenleaf

state: CA

address: 279 Campus Drive West

department: Genetics

institute: Stanford University

description: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep).

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks were called on single cell ATAC-seq data from this series as well as GSE65360 and GSE74310 using MACS2.  Peak summits were called on merged bamfiles from each different celltype, fixed to 500bp around the summit, and then combined. Fragments with either end mapping inside the peak were counted for each cell for each peak.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.
scATAC-seq

value: cell line, chronic myelogenous leukemia, untreated


title: singles-K562-141106-94


title: singles-K562-141106-95


title: singles-K562-141106-96


title: singles-K562-141106-93


title: singles-K562-141106-91


title: F. tularensis treated with human erythrocyte, replicate 3


title: singles-K562-141106-88


title: singles-K562-141106-86


title: singles-K562-141106-90


title: singles-K562-141106-85


title: singles-K562-141106-89


title: singles-K562-141106-84


title: singles-K562-141106-82


title: singles-K562-141106-87


title: singles-K562-141106-9


title: singles-K562-141106-80


title: singles-K562-141106-81


title: singles-K562-141106-83


title: singles-K562-141106-79


title: F. tularensis control treated, replicate 1


title: singles-K562-141106-8


title: ath_circRNA 1.14

source_name: ath circRNA 1.14


title: singles-K562-141106-78


title: singles-K562-141106-75


title: singles-K562-141106-77


title: singles-K562-141106-76


title: singles-K562-141106-73


title: singles-K562-141106-72


title: singles-K562-141106-74


title: singles-K562-141106-70


title: singles-K562-141106-69


title: singles-K562-141106-67


title: singles-K562-141106-7


title: singles-K562-141106-71


title: singles-K562-141106-66


title: singles-K562-141106-68


title: singles-K562-141106-6


title: singles-K562-141106-61


title: singles-K562-141106-63


title: singles-K562-141106-64


title: singles-K562-141106-62


title: singles-K562-141106-60


title: singles-K562-141106-65


title: singles-K562-141106-53


title: singles-K562-141106-59


title: singles-K562-141106-54


title: singles-K562-141106-58


title: singles-K562-141106-57


title: singles-K562-141106-55


title: singles-K562-141106-56


title: singles-K562-141106-51


title: singles-K562-141106-52


title: singles-K562-141106-5


title: singles-K562-141106-48


title: singles-K562-141106-47


title: singles-K562-141106-50


title: singles-K562-141106-49


title: singles-K562-141106-46


title: singles-K562-141106-41


title: singles-K562-141106-45


title: singles-K562-141106-44


title: singles-K562-141106-40


title: singles-K562-141106-39


title: singles-K562-141106-4


title: singles-K562-141106-35


title: singles-K562-141106-38


title: singles-K562-141106-36


title: singles-K562-141106-37


title: singles-K562-141106-28


title: singles-K562-141106-3


title: singles-K562-141106-34


title: singles-K562-141106-32


title: singles-K562-141106-33


title: singles-K562-141106-29


title: singles-K562-141106-31


title: singles-K562-141106-25


title: singles-K562-141106-30


title: singles-K562-141106-22


title: singles-K562-141106-26


title: singles-K562-141106-27


title: singles-K562-141106-21


title: singles-K562-141106-23


title: singles-K562-141106-24


title: singles-K562-141106-20


title: singles-K562-141106-19


title: singles-K562-141106-42


title: singles-K562-141106-43


title: singles-K562-141106-18


title: singles-K562-141106-17


title: singles-K562-141106-16


title: singles-K562-141106-15


title: singles-K562-141106-14


title: singles-K562-141106-13


title: singles-K562-141106-10


title: singles-K562-141106-11


title: singles-K562-141106-12


title: singles-K562-141106-1


title: singles-K562-141105-94


title: singles-K562-141105-9


title: singles-K562-141105-89


title: singles-K562-141105-96


title: singles-K562-141105-88


title: singles-K562-141105-91


title: singles-K562-141105-92


title: singles-K562-141106-2


title: singles-K562-141105-90


title: singles-K562-141105-86


title: singles-K562-141105-82


title: singles-K562-141105-83


title: singles-K562-141105-84


title: singles-K562-141105-87


title: singles-K562-141105-85


title: singles-K562-141105-93


title: singles-K562-141105-81


title: singles-K562-141105-80


title: singles-K562-141105-8


title: singles-K562-141105-79


title: singles-K562-141105-78


title: singles-K562-141105-74


title: singles-K562-141105-95


title: singles-K562-141105-73


title: singles-K562-141105-71


title: singles-K562-141105-70


title: singles-K562-141105-68


title: singles-K562-141105-69


title: singles-K562-141105-67


title: singles-K562-141105-65


title: singles-K562-141105-66


title: singles-K562-141105-64


title: singles-K562-141105-63


title: singles-K562-141105-58


title: singles-K562-141105-56


title: singles-K562-141105-62


title: singles-K562-141105-55


title: singles-K562-141105-54


title: singles-K562-141105-57


title: singles-K562-141105-53


title: singles-K562-141105-6


title: singles-K562-141105-76


title: singles-K562-141105-51


title: singles-K562-141105-52


title: singles-K562-141105-75


title: singles-K562-141105-72


title: singles-K562-141105-7


title: singles-K562-141105-5


title: singles-K562-141105-50


title: singles-K562-141105-48


title: singles-K562-141105-61


title: singles-K562-141105-59


title: singles-K562-141105-60


title: singles-K562-141105-46


title: singles-K562-141105-43


title: singles-K562-141105-42


title: singles-K562-141105-44


title: singles-K562-141105-40


title: singles-K562-141105-4


title: singles-K562-141105-45


title: singles-K562-141105-39


title: RA_T-01

city: Nanjing

first: Lufan

last: Li

address: No.101 Longmian Blvd

institute: Nanjing Medical University

data_processing:
Illumina OLB1.9.4 software used for basecalling.
Primary sequencing data that produced by Illumina HiSeqTM 2000, is subjected to quality control (QC) that determine if a resequencing step is needed. raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis. If alignment result passes QC, we will proceed with downstream analysis including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation and SNP detection.
Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Annotations in processed data file are located at www.noncode.org
Genome_build: NONCODE v3.0
Supplementary_files_format_and_content: tab-delimited text files include reads numbers、Length、 RPKM values for each Sample

source_name: Testis

growth_protocol: Germ cells were isolated from 6- to 8-day-old C57BL/6 and Thy1-positive cells were enriched using magnetic-activated cell separation. Cells were plated at a density of 1.5 to 2×105 per well on 12-well plates with mitotically inactivated STO feeder layers and cultured in a defined serum-free medium consisting of minimal essential medium supplemented with 2% bovine serum albumin, 20 ng/ml GDNF, 150 ng/ml GFRA1 and 1 ng/ml bFGF, 10 μg/ml transferrin, 50 μM free fatty acid mixture, 30 nM Na2SeO3, 2 mM L-glutamine, 50 μM 2-mercaptoethano, 5 μg/ml insulin (Sigma-Aldrich), 10 mM HEPES and 60 μM putrescine. Cultures were maintained at 37 ℃in an incubator with humidified 5% CO2 and 95% air atmosphere. Medium was replaced every 2–3 days and cells were passaged at a ratio of 1 : 2 or 1 : 3 every 5 to 6 days

extract_protocol:
After Retinoic acid treatment, SSCs were collected by a pipetting method, followed the standard total RNA extraction protocol using Trizol Regent.
RNA libraries for sequencing  were prepared using standard Illumina protocols

value: spermatogonial stem cells

tag: treatment

value: trans-retinoic acid(0.3mM in 0.1% EtOH)


title: RA_C-02

value: vehicle solution(0.1% EtOH)


title: singles-K562-141105-37


title: singles-K562-141105-38


title: singles-K562-141105-35


title: singles-K562-141105-36


title: singles-K562-141105-77


title: singles-K562-141105-49


title: RA_C-01


title: singles-K562-141105-47


title: singles-K562-141105-34


title: Whsc1_pB_KO1

city: Madrid

first: Cesar

last: Cobaleda

address: c/Nicolas Cabrera, 1

country: Spain

institute: CBM, CSIC

data_processing:
Alignment and quantification. RNA-seq reads were aligned to the mouse reference genome (GRCm38) using STAR (version 2.5.1b)(Dobin et al., 2013) with default ENCODE parameters. Genes were quantified using RSEM (version 1.2.28)(Li and Dewey, 2011) with default parameters. Mouse gene annotation file was downloaded from gencode release vM9 (http://www.gencodegenes.org/).
Differential gene expression. RSEM gene counts was used as input for the DESeq2 R package (version 1.10.1)(Love et al., 2014) for WT vs KO comparison adding sex as a covariate in the model. DESeq2 was run with default parameters. Genes with FDR<5% were considered significant.
Enrichment Analyses. Gene ontology and KEGG enrichment analysis were performed with DAVID db(Huang da et al., 2009).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file including normalized values for each sample. Excel file including DGE data and results from pathway analyses.

source_name: FACS sorted BM proB cells

growth_protocol: We sorted B220+CD19+ckit+CD25-PI- proB cells form the BM of mice injected with either WT or Whsc1-/- cells.

extract_protocol:
RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. Its chemical quality was measured by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer.
Sorted proB cells RNA sequencing (low input RNA-seq). RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2013) with minor modifications. Briefly, RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and 3.2-30.6 ng of RNA was used for cDNA synthesis. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), template-switching oligonucleotides (1µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), 100 nM ISPCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 20 cycles of amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent). 200 ng of the amplified cDNA was fragmented for 10 min at 55 ºC using Nextera® XT (Illumina) and amplified for 12 cycles with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified again on a Bioanalyzer using a High Sensitvity DNA Kit. Sequencing of Nextera® libraries was carried out using fraction of a sequencing lane on a HSeq2000 (Illumina inc.) using TruSeq SBS Kit v3-HS, and between 74-80 million paired-end reads were generated for each sample. The read length was 101bp with TruSeq Dual Index of 8bp+8bp. Images analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA 1.8.

value: bone marrow proB cells


title: WT_pB_rep2

value: WT


title: singles-K562-141105-33


title: Whsc1_pB_KO3


title: WT_pB_rep1


title: singles-K562-141105-41


title: Whsc1_KO6

description:
Whsc1_norm_counts
Whsc1_DE

data_processing:
Alignment and quantification. RNA-seq reads were aligned to the mouse reference genome (GRCm38) using STAR (version 2.5.1b)(Dobin et al., 2013) with default ENCODE parameters. For female samples the Y chromosome was removed from the reference before the mapping. Genes were quantified using RSEM (version 1.2.28)(Li and Dewey, 2011) with default parameters. Mouse gene annotation file was downloaded from gencode release vM9 (http://www.gencodegenes.org/).
Differential gene expression. RSEM gene counts was used as input for the DESeq2 R package (version 1.10.1)(Love et al., 2014) for WT vs KO comparison adding sex as a covariate in the model. DESeq2 was run with default parameters. Genes with FDR<5% were considered significant.
Enrichment Analyses. Gene ontology and KEGG enrichment analysis were performed with DAVID db(Huang da et al., 2009).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file including RPKM values for each sample. Excel file including DGE data and results from pathway analyses.

source_name: LPS-stimulated splenic B cells

growth_protocol: Mouse primary B cells were purified from the spleens of the indicated strains of mice by immunomagnetic depletion with anti-CD43 beads [Miltenyi Biotec] and were cultured in 50 µM 2-β-Mercaptoethanol (Invitrogen), 10 mM Hepes [Invitrogen], 1 mM Glutamine, antibiotics, Non-Essential Aminoacids and 10% HI-FBS RPMI medium, supplemented with 25 µg/ml LPS [Sigma-Aldrich], for 48 h.

extract_protocol:
RNA was extracted following commercial Trizol® Reagent [Cat No 15596-026, Life TecnologiesTM, GibcoBRL] recommendations. It chemical quality was measure by Nanodrop 1000 Spectrophotometer [Thermo ScientificTM] and it integrity was confirmed using the Agilent 2100 Bioanalyzer.
The libraries from the mouse total RNA were prepared using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013) according to manufacturer’s protocol. Briefly, 0.5 µg of total RNA was used for poly-A based mRNA enrichment with oligo-dT magnetic beads. The mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v3-HS. We generated about 50-70 million paired-end reads for each sample in a fraction of a sequencing flowcell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.

tag: genotipe


title: Whsc1_KO5

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-32


title: RA_T-02


title: Whsc1_KO4

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-31


title: Whsc1_KO1

description:
Whsc1_norm_counts
Whsc1_DE


title: Whsc1_KO2

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-29


title: Whsc1_KO3

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-30


title: WT_rep7

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-27


title: singles-K562-141105-28


title: WT_rep6

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-26


title: singles-K562-141105-25


title: singles-K562-141105-24


title: WT_rep5

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-23


title: singles-K562-141105-20


title: WT_rep4

description:
Whsc1_norm_counts
Whsc1_DE


title: WT_rep3

description:
Whsc1_norm_counts
Whsc1_DE


title: WT_rep2

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-22


title: singles-K562-141105-19


title: WT_rep1

description:
Whsc1_norm_counts
Whsc1_DE


title: singles-K562-141105-18


title: singles-K562-141105-21


title: singles-K562-141105-3


title: ChAT_posterior_cell_5

city: Seattle

first: Thuc Nghi

last: Nguyen

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

data_processing:
Adapter sequences were clipped from 100  or 75 base-pair single-end reads in FASTQ format using the ea-utils application fastq-mcf with settings -C 200000 to filter against Nextera adapter sequences.
Trimmed reads were aligned to GRCm38 (mm10) using the RefSeq annotation gff file downloaded on 6/1/2013. Transcriptome alignment files in BAM format were generated with RSEM v1.2.4 and Bowtie v1.1.0 using the program rsem-calculate-expression with settings --keep-intermediate-files --bowtie-chunkmbs 2000 --output-genome-bam --bowtie-e 500 --bowtie-m 100.
Reads that did not map to the RefSeq annotations were aligned to ERCC sequences, tdTomato sequence, and nls-YFP-WPRE sequence using Bowtie v1.1.0 with settings -S --chunkmbs 2000.
Genome_build: mm10
Supplementary_files_format_and_content: CSV: Comma-separated tables of data values; Columns are samples and Rows are genes or ERCC/tdTomato. Column names correspond to sample Titles; Row names correspond to RefSeq Gene Symbols, ERCC symbols, or tdTomato.

source_name: preopic area neuron

growth_protocol: Animals were provided food and water ad libitum and were maintained at a regular 12 h day/night cycle at no more than 5 adult animals per cage. Animals were maintained on the C57BL/6J background.

extract_protocol:
Individual adult male mice (P47-66) were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in fresh ice-cold artificial cerebrospinal fluid (ACSF). The brain was sectioned on a vibratome (Leica VT1000S) on ice, and each slice (300-400 µm) was immediately transferred to an ACSF bath at room temperature. After the brain slicing is complete (not more than 15 minutes), individual slices of interest were transferred to a small Petri dish containing bubbled room temperature ACSF. The regions of interest were microdissected under a fluorescence dissecting microscope. The dissected tissue pieces were transferred to a microcentrifuge tube and treated with 1 mg/ml pronase in carbogen-bubbled ACSF for 70 minutes at room temperature without mixing in a closed tube. After incubation, with the tissue pieces sitting at the bottom of the tube, the pronase solution was pipetted out of the tube and exchanged with cold ACSF containing 1% fetal bovine serum. The tissue pieces were dissociated into single cells by gentle trituration through Pasteur pipettes with polished tips of 600, 300, and 150-µm diameter. Single cells were isolated by FACS into individual wells of 96-well plates or 8-well PCR strips containing 2.275 µl of Dilution Buffer (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936), 0.125 µl RNase inhibitor (SMARTer kit), and 0.1 µl of 1:1,000,000 diluted RNA spike-in RNAs (ERCC RNA Spike-In Mix 1, Life Technologies Cat#4456740). Sorting was performed on a BD FACSAriaII SORP using a 130um nozzle, a sheath pressure of 10psi, and in the single cell sorting mode. To exclude dead cells, DAPI (DAPI*2HCl, Life Technologies Cat#D1306) was added to the single cell suspension to the final concentration of 2 ng/ml. FACS populations were chosen to select cells with low DAPI and high YFP fluorescence (for SADB-rEIAV-tloop-DIO-nls-YFP injected animals) or  tdTomato (tdT) fluorescence (for Chat-IRES-Cre;Ai14 animals). Sorted cells were frozen immediately on dry ice and stored at -80°C.
We used the SMARTer kit from Clontech (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936)  to reverse transcribe single cell RNA, and amplify the cDNA for 19 PCR cycles. To stabilize the RNA after quickly thawing the cells on ice, we immediately added to each sample an additional 0.125 µl of RNase inhibitor mixed with SMART CDS Primer II A. All steps downstream were carried out according to the manufacturer’s instructions. Each amplification experiment included a set of controls: 10 pg cortex RNA (isolated from Rbp4-Cre;Ai14, P57 male) as positive control for amplification, ERCC-only control to demonstrate the absence of RNases throughout the sorting process, and water-only control, to control for specificity of amplification/absence of contamination. cDNA concentration was quantified using Agilent Bioanalyzer High Sensitivity DNA chips. For most samples, 1 ng of amplified cDNA was used as input to make sequencing libraries with Nextera XT DNA kit (Illumina Cat#FC-131-1096).  We stopped the procedure after PCR clean-up and did not perform library normalization or library pooling. Individual libraries were quantified using Agilent Bioanalyzer DNA 7500 chips. In order to assess sample quality and adjust the concentrations of libraries for multiplexing on HiSeq or NextSeq. Libraries were sequenced on Illumina HiSeq single end 100-bp or NextSeq single end 75-bp.

treatment_protocol: We injected SADB-rEIAV-tloop-DIO-nls-YFP into brains of Gad2-IRES-Cre or Slc32a1-IRES-Cre mice. Briefly, mice were anesthetized with 5% isoflurane and then placed into a stereotaxic alignment instrument (Kopf, model 1900). Anesthesia was maintained for the duration of the surgery by administering isoflurane at 1-2% through a nose cone. The skin along the midline of the skull was opened using a scalpel, and a surgical drill was used to create a small hole in the skull. A pulled glass pipette prefilled with virus solution was lowered into the brain, and 500-700 nl of the virus solution was delivered to the targeted brain area using a pressure injection system (NanoJect II, Drummond Scientific Company, Catalog# 3-000-204). Stereotaxic coordinates were obtained from Paxinos adult mouse brain atlas for tuberomammillary nucleus (TMN, AP -2.45 mm, ML 1 mm, DV 5-5.2 mm). After the delivery of virus solution into the brain, the glass pipette was retracted and the incision in the scalp was closed using sutures. The animal was removed from the stereotaxic frame and allowed to recover from anesthesia. Mice were sacrificed 15−28 days after surgery for single cell isolation. YFP+ single cells were isolated from the preoptic area.

tag: mouse line abbreviation

value: Chat

tag: cre driver

value: Chat-IRES-Cre

tag: reporter

value: RCL-tdT (Ai14)

tag: brain region

value: preoptic area

tag: dissection

value: posterior

tag: input material

value: single cell

tag: tdtomato labeling

value: Y

tag: yfp labeling

tag: passes qc checks

tag: animal id


title: ChAT_posterior_cell_6


title: ChAT_posterior_cell_7


title: ChAT_posterior_cell_8


title: singles-K562-141105-2

tag: cell type


title: ChAT_posterior_cell_4


title: singles-K562-141105-15


title: singles-K562-141105-14


title: ChAT_posterior_cell_2


title: ChAT_posterior_cell_1


title: VGAT_anterior_cell_32

value: SADB-rEIAV-tloop-DIO-nls-YFP

value: anterior


title: singles-K562-141105-17


title: singles-K562-141105-13


title: singles-K562-141105-16


title: VGAT_anterior_cell_31


title: singles-K562-141105-10


title: VGAT_anterior_cell_30


title: singles-K562-141105-1


title: singles-K562-141104-95


title: singles-K562-141104-94


title: VGAT_anterior_cell_29


title: VGAT_anterior_cell_27


title: singles-K562-141104-96


title: singles-K562-141104-91


title: singles-K562-141104-93


title: VGAT_anterior_cell_28


title: singles-K562-141105-11


title: singles-K562-141104-92


title: singles-K562-141104-90


title: ChAT_posterior_cell_3


title: singles-K562-141104-86


title: singles-K562-141104-87


title: singles-K562-141104-9


title: singles-K562-141104-80


title: singles-K562-141104-89


title: singles-K562-141104-84


title: singles-K562-141104-88


title: singles-K562-141104-83


title: singles-K562-141104-81


title: singles-K562-141104-82


title: singles-K562-141104-79


title: singles-K562-141105-12


title: singles-K562-141104-76


title: singles-K562-141104-77


title: singles-K562-141104-75


title: singles-K562-141104-73


title: singles-K562-141104-74


title: singles-K562-141104-70


title: singles-K562-141104-7


title: singles-K562-141104-71


title: singles-K562-141104-72


title: singles-K562-141104-8


title: singles-K562-141104-68


title: singles-K562-141104-67


title: singles-K562-141104-66


title: singles-K562-141104-78


title: singles-K562-141104-62


title: singles-K562-141104-85


title: singles-K562-141104-60


title: singles-K562-141104-58


title: singles-K562-141104-56


title: singles-K562-141104-6


title: singles-K562-141104-65


title: singles-K562-141104-51


title: singles-K562-141104-64


title: singles-K562-141104-63


title: singles-K562-141104-69


title: singles-K562-141104-59


title: singles-K562-141104-61


title: singles-K562-141104-55


title: singles-K562-141104-52


title: singles-K562-141104-53


title: singles-K562-141104-50


title: singles-K562-141104-46


title: singles-K562-141104-43


title: singles-K562-141104-42


title: singles-K562-141104-47


title: singles-K562-141104-41


title: singles-K562-141104-39


title: singles-K562-141104-57


title: singles-K562-141104-40


title: singles-K562-141104-54


title: singles-K562-141104-38


title: singles-K562-141104-44


title: singles-K562-141104-45


title: singles-K562-141104-37


title: singles-K562-141104-33


title: singles-K562-141104-34


title: singles-K562-141104-35


title: singles-K562-141104-31


title: singles-K562-141104-32


title: singles-K562-141104-30


title: singles-K562-141104-29


title: singles-K562-141104-3


title: singles-K562-141104-27


title: singles-K562-141104-48


title: singles-K562-141104-5


title: singles-K562-141104-24


title: singles-K562-141104-26


title: singles-K562-141104-25


title: singles-K562-141104-28


title: singles-K562-141104-49


title: singles-K562-141104-23


title: singles-K562-141104-2


title: singles-K562-141104-4


title: singles-K562-141104-22


title: singles-K562-141104-36


title: singles-K562-141104-21


title: singles-K562-141104-19


title: singles-K562-141104-18


title: singles-K562-141104-17


title: singles-K562-141104-15


title: singles-K562-141104-14


title: singles-K562-141104-13


title: singles-K562-141104-11


title: singles-K562-141104-1


title: singles-K562-141104-12


title: singles-K562-141104-10


title: non silencing shRNA-transduced H929-2

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Alignment was done by using STAR_2.3.0. GRCh37 reference genome was used
samtools-0.1.19 was used for SAM to BAM conversion and sorting the files.
rMATS.3.2.5 was used for alternative splicing events with same GTF file from gene quantification step
featureCounts from subread-1.4.6-p2-Linux-x86_64 was used to quantify the raw counts with Homo_sapiens.GRCh37.75.gtf.
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files with count data.

source_name: Multiple Myeloma

growth_protocol: RPMI+ 10% PBS

extract_protocol:
RNA was extrated using the Rneasy Mini Kit (Qiagen)
Libraries were constructed using the the TruSeq® Stranded Total RNA LT - (with Ribo-Zero TM Gold) - Set A (Illumina) . Transcriptomic RNA-Seq was performed on the 2000 Illumina HiSeq platform using the standard paired-end protocol. In total, 60-160 million 76-bp reads were generated per sample.

tag: cell line

value: Multiple myeloma


title: non silencing shRNA-transduced H929-1


title: ILF2 shRNA-transduced H929-1


title: singles-K562-141104-20


title: JJN3 melphalan treated 1 [YB-1]

data_processing:
Raw data alignment was done with STAR_2.3.0e_r291 with --outFilterMismatchNmax 4 --outSAMstrandField intronMotif parameters
FPKM values and isoform analysis was done with Cuffdiff v 2.2.1 by using Gencode v22 annotation
Supplementary_files_format_and_content: FPKM values

source_name: JJN3 melphalan treated

extract_protocol:
RNA immunoprecipitation was performed using the Magna RIP RNA-binding protein immunoprecipitation kit (Millipore) according to the manufacturer’s instructions.
Libraries were constructed using the Ovation RNA-Seq System V2 (Nugen)
Transcriptomic RNA-Seq was performed on the Illumina HiSeq platform using the standard paired-end protocol

treatment_protocol: 25μM melphalan

value: Multiple Myeloma

tag: treated with

value: 25μM melphalan

tag: rip antibody


title: ILF2 shRNA-transduced H929-2


title: JJN3 input melphalan treated 1 [YB-1]

source_name: JJN3 input melphalan treated


title: JJN3 melphalan treated 2 [YB-1]


title: JJN3 untreated 1 [YB-1]

source_name: JJN3 untreated

value: none (untreated)


title: JJN3 untreated 2 [YB-1]


title: H929 untreted input 2

description: 4-H929 WT input

source_name: H929 untreted input


title: H929 input melphalan treated 1

description: 1-H929 melphalan input

source_name: H929 input melphalan treated


title: H929 untreated input 1

description: 3-H929 WT input

source_name: H929 untreated input


title: H929 melphalan treated 2

description: 10-H929 melphalan

source_name: H929 melphalan treated

value: anti-ILF2 (Abcam, ab113205, lot GR57404-8)


title: JJN3 untreated input 1 [YB-1]

description: NS-input

source_name: JJN3 untreated input


title: H929 untreated 1

description: 11-H929 WT

source_name: H929 untreated


title: singles-K562-141104-16

value: cell line, chronic myelogenous leukemia, untreated


title: H929 untreated 2

description: 12-H929 WT


title: H929 melphalan treated 1

description: 9-H929 melphalan


title: JJN3 input melphalan treated 2

description: 6-JJN3 melphalan input


title: JJN3 untreated input 1

description: 7-JJN3 WT input


title: JJN3 input melphalan treated 1

description: 5-JJN3 melphalan input


title: JJN3 untreted input 2

description: 8-JJN3 WT input

source_name: JJN3 untreted input


title: JJN3 melphalan treated 2


title: JJN3 melphalan treated 1


title: JJN3 untreated 1

description: 15-JJN3 WT


title: JJN3 untreated 2

description: 16-JJN3 WT


title: H1299_P_Input

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
ChIP-seq reads were aligned to hg19 geneome assembly using Bowtie (v.2.2.5)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Normalized bigwig files were generated by subtracting the input signal from ChIP signal using HOMER (v.4.7)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contains ChIP signal subtracted from input in bigwig format

source_name: NCI-H1299 cell line

growth_protocol: NSCLC cell lines were maintained in RPMI-1640 (Life Technologies Inc.) with 5% FBS.

extract_protocol:
Drug treated H1299 Parental and H1299 T18 cells at 80% confluency (~10 million cells) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. Following ice-cold PBS wash, the cell pellets were resuspended in 1.5 ml ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 2 x 15 minutes). The chromatin predominantly sheared to a fragment length of ~250 – 750 bp was centrifuged at 20,000 g for 15 minutes at 4°C. 100 μl of the supernatant was used for ChIP, and DNA purified from 30 μl of sheared chromatin was used as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 10 μg of a mouse monoclonal anti-histone H3K27me3 antibody (Abcam, cat# ab6002) or a rabbit polyclonal anti-histone H3K4me3 antibody (Millipore, cat# 07-473). Immunoprecipitation was carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl, protease inhibitors; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl, protease inhibitors; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments from immunoprecipitated chromatin and input were purified using QiaQuick PCR Purification kit (QIAGEN) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.
Barcoded libraries of ChIP and input DNA were generated with the TruSeq® ChIP Sample Preparation Kit (Illumina).

treatment_protocol: H1299 Parental and H1299 T18 cells were treated for 24 h with either DMSO control, 1 µM GSK-J4 or 0.2 µM JIB-04.

value: H1299 Parental

tag: antibody


title: H929 input melphalan treated 2

description: 2-H929 melphalan input


title: H1299_T18_GSK_J4_H3K4

source_name: H1299 T18 cell line

tag: treatment

value: H1299 T18 cells treated with GSK-J4

value: rabbit polyclonal anti-histone H3K4me3 antibody (Millipore, cat# 07-473)


title: H1299_T18_JIB04_H3K27

value: H1299 T18 cells treated with JIB-04

value: mouse monoclonal anti-histone H3K27me3 antibody (Abcam, cat# ab6002)


title: H1299_T18_GSK_J4_H3K27


title: H1299_T18_DMSO_H3K4

value: H1299 T18 cells treated with DMSO


title: H1299_T18_JIB04_H3K4


title: Activated+CsA NFAT1 ChIP

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
The custom barcodes were removed from the reads using a custom script.
The ChIP-seq sequencing libraries were mapped against mm9 using Bowtie.
Reads with identical sequences were filtered and only one was retained for subsequent analysis.
Enriched (relative to inputs) regions in ChIP samples were detected using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: NFAT1 binding sites (bed)

source_name: Memory-like CTLs

growth_protocol: Naïve CD8 T cells were stimulated with anti-CD3 and anti-CD28. On day 2, cells were removed from the initial stimulus and expanded with IL-2 (10U/ml) every day. Each day, cells were cultured at 5x10^5 cells/ml. On day 6, cells were either left untreated or restimulated with PMA and Ionomycin in the presence of DRB or CsA.

extract_protocol:
Sonicated chromatin was obtained and incubated with anti-NFAT1/proteinG beads
SOLID

treatment_protocol: Restimulation with PMA/Ionomycin in the presence of CsA (Calcineurin inhibitor) or DRB (pTEFb inhibitor)

tag: strain

tag: tissue

value: spleen/lymph nodes-isolated naive CD8 T cells

tag: chip antibody

value: anti-mouse NFAT1 (67.1)


title: Activated+DRB NFAT1 ChIP


title: H1299_T18_Input


title: H1299_T18_DMSO_H3K27


title: H1299_P_JIB04_H3K4

value: H1299 Parental cells treated with JIB-04


title: Activated+DRB input


title: H1299_P_GSK_J4_H3K27

value: H1299 Parental cells treated with GSK-J4


title: H1299_P_JIB04_H3K27


title: Resting NFAT1 ChIP


title: Activated NFAT1 ChIP


title: H1299_P_GSK_J4_H3K4


title: Activated+CsA input


title: H1299_P_DMSO_H3K27

value: H1299 Parental cells treated with DMSO


title: H1299_P_DMSO_H3K4


title: Activated input


title: Resting input


title: T18_GSKJ4_rep1

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to hg19 geneome assembly and transcript assembly was performed using tophat (v.2.0.13)
RPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H1299 Parental and H1299 T18 cells were treated for 24 h with either DMSO control or 1 µM GSK-J4.

tag: histology

value: NSCLC, Large cell carcinoma

tag: age

tag: gender

value: M

tag: race

value: Caucasian

tag: smoking status

value: Smoker

tag: pack-years

value: T18 resistant cells treated with GSKJ4


title: T18_GSKJ4_rep2


title: T18_DMSO_rep2

value: T18 resistant cells treated with DMSO


title: T18_DMSO_rep1


title: P_GSKJ4_rep2

value: Parental cells treated with GSKJ4


title: P_GSKJ4_rep1


title: P_DMSO_rep2

value: Parental cells treated with DMSO


title: P_DMSO_rep1


title: DU145 with shRNA NUSAP #2 knockdown 96 hrs Rep 3

first: James

middle: D.

last: Brooks

address: 300 Pasteur Drive

department: Urology

description: Knockdown_NUSAP1_using_shRNA_2_for_96_hours_in_DU145_cells.txt

data_processing:
mapping by Tophat v2.0.0 using default parameters
quantilifcation by Cufflinks v2.0.2 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: prostatic carcinoma

extract_protocol:
Total RNA from DU145 or PC-3 cells grown in 6-well plates was purified using TRIzol Reagent (Life Technologies) as directed by the manufacturer’s protocol. To further cleanup RNA, the RNeasy MinElute Cleanup Kit (Qiagen) was used as directed by the manufacturer’s protocol.
RNA libraries were prepared with the TruSeq RNA Sample Preparation Kit v2 (Illumina) or TruSeq Stranded mRNA Sample Preparation Kit (Illumina) using 1 µg of total RNA as directed by the manufacturer’s protocol.

tag: passages

tag: tumor

value: prostatic carcinoma

value: prostate brain metastasis

tag: genotype/variation

value: shRNA NUSAP #2 knockdown 96 hrs


title: DU145 with shRNA NUSAP #2 knockdown 96 hrs Rep 2


title: DU145 with shRNA NUSAP #1 knockdown 96 hrs Rep 3

description: Knockdown_NUSAP1_using_shRNA_1_for_96_hours_in_DU145_cells.txt

value: shRNA NUSAP #1 knockdown 96 hrs


title: MCF10CA1a Hi-C REP 2

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
MCF10CA1a_pooled_40000_iced.matrix.gz
HiCPro_40000_matrix_coordinates.bed
MCF10CA1a_pooled.allValidPairs.hic

data_processing:
Fastq conversion and demultiplexing were done using bcl2fastq (Illumina, v1.8.4)
Reads were aligned to canonical hg38 chromosomes using HiC-Pro 2.8.1 calling bowtie2 2.1.0 with HiC-Pro’s default options.
The merged allValidPairs files were converted to .hic for JuiceBox using HiC-Pro's hicpro2juicebox.sh script (juicer tools 0.7.5, adapted to set 40kb resolution chr6 only).
Genome_build: hg38
Supplementary_files_format_and_content: .matrix files are 40kb resolution iced matrix files from HiC-Pro.
Supplementary_files_format_and_content: HiCPro_40000_matrix_coordinates.bed is a bed formatted file to convert indexes of iced matrices to genomic coordinates.
Supplementary_files_format_and_content: .hic files are 40kb resolution interaction files of chr6 for input to JuiceBox.

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10A and MCF10AT1 cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10CA1a cells were grown in DMEM: F12 (Hyclone-SH30271) + 5% (v/v) horse serum (Gibco #16050) +Pen/Strep (Life Technologies)and Glutamine (Life Technologies)  .

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
DNA libraries were prepared for sequencing using standard Illumina TruSeq ChIP kit (Illumina #IP-202-1012)
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and paired-end 100-base (PE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1x106 cells per 100 mm dish and grown to 80-90% confluence. Cells were washed twice with phosphate buffered saline (PBS), fixed with 1% methanol free formaldehyde, and pellets stored at -80C. Hi-C was performed as previously published (belton, 2012, PMCID: PMC3874846).

value: breast

tag: cell type

value: basal, metastatic

tag: neoplasia type

value: tumorigenic

tag: atcc id


title: DU145 with shRNA NUSAP #1 knockdown 96 hrs Rep 2


title: CH1

city: beijing

first: Yawen

last: Zhang

address: No. 2 Yuanmingyuan West Rd.

institute: china agriculture university

description:
processed data file:
CHH.peaks.wig

data_processing:
Basecalls performed using Illumina CASAVA version 1.8.4
Raw sequencing data were filtered by removing the adaptors and discarding low quality reads that contained more than 10 % of undetermined bases (N) or over 40 % of low-quality bases (Qphred ≤ 20), then were aligned to the chicken reference genome (version 4.74) using SOAP2 (version 2.21) with no more than five mismatched bases.
Peaks were called using MACS1.4.0 with parameters --pvalue 1e-3 --bw 200 model fold = 5,30
Genome_build: galGal4; GCF_000002315.3

organism: Gallus gallus

source_name: lowland Chahua_Embryonic heart tissue

growth_protocol: Eggs of Tibetan chicken (TC) and Chahua chicken (CH) were collected . The eggs were placed in a hypoxic (13 % O2) incubator, with a temperature and humidity of 37.8 °C and 60 %, respectively. Embryo heart tissue was collected after 16 d under incubation

extract_protocol:
The genomic DNA from the heart tissue was extracted using the phenol–chloroform method and sonicated to obtain fragments in the range of 100–500 bp. The double-stranded DNA was denatured and subsequently immunoprecipitated with an antibody that specifically recognizes 5′-methylcytosine using a Magnetic Methylated DNA Immunoprecipitation Kit(Diagenode).
Libraries were prepared according to the Illumina’s Paired-End DNA Sample Prep kit.

tag: breed

value: lowland Chahua chicken

tag: developmental stage

value: 16d embryo

value: heart


title: TC2

description:
processed data file:
TCH.peaks.wig

source_name: highland Tibetan_Embryonic heart tissue

value: highland Tibetan chicken


title: TC1

description:
processed data file:
TCH.peaks.wig


title: DU145 with shRNA NUSAP #1 knockdown 96 hrs Rep 1


title: MCF10CA1a Hi-C REP 1


title: MCF10AT1 Hi-C REP 2

description:
MCF10AT1_pooled_40000_iced.matrix.gz
HiCPro_40000_matrix_coordinates.bed
MCF10AT1_pooled.allValidPairs.hic

value: basal, pre-metastatic

value: hyperplastic


title: TC3

description:
processed data file:
TCH.peaks.wig


title: DU145 with Scramble knockdown 96 hrs Rep2

description:
Knockdown_NUSAP1_using_shRNA_1_for_96_hours_in_DU145_cells.txt
Knockdown_NUSAP1_using_shRNA_2_for_96_hours_in_DU145_cells.txt

value: Scramble knockdown 96 hrs


title: CH3

description:
processed data file:
CHH.peaks.wig


title: CH2

description:
processed data file:
CHH.peaks.wig


title: DU145 with shRNA NUSAP #2 knockdown 72 hrs Rep 2

description: Knockdown_NUSAP1_using_shRNA_2_for_72_hours_in_DU145_cells.txt

value: shRNA NUSAP #2 knockdown 72 hrs


title: DU145 with shRNA NUSAP #2 knockdown 72 hrs Rep 3


title: DU145 with shRNA NUSAP #2 knockdown 72 hrs Rep 1


title: DU145 with shRNA NUSAP #1 knockdown 72 hrs Rep 3

description: Knockdown_NUSAP1_using_shRNA_1_for_72_hours_in_DU145_cells.txt

value: shRNA NUSAP #1 knockdown 72 hrs


title: MCF10AT1 Hi-C REP 1


title: DU145 with shRNA NUSAP #1 knockdown 72 hrs Rep 2


title: DU145 with Scramble knockdown 96 hrs Rep1


title: DU145 with shRNA NUSAP #1 knockdown 72 hrs Rep 1


title: DU145 with Scramble knockdown 72 hrs Rep3

description:
Knockdown_NUSAP1_using_shRNA_1_for_72_hours_in_DU145_cells.txt
Knockdown_NUSAP1_using_shRNA_2_for_72_hours_in_DU145_cells.txt

value: Scramble knockdown 72 hrs


title: DU145 with Scramble knockdown 72 hrs Rep2

value: prostatic carcinoma


title: PC-3 with shRNA NUSAP #2 knockdown 96 hrs Rep 3

description: Knockdown_NUSAP1_using_shRNA_2_for_96_hours_in_PC3_cells.txt

source_name: prostatic adenocarcinoma

value: prostatic adenocarcinoma

value: prostate bone metastasis


title: DU145 with Scramble knockdown 72 hrs Rep1

value: prostate brain metastasis


title: PC-3 with shRNA NUSAP #2 knockdown 96 hrs Rep 2

value: shRNA NUSAP #2 knockdown 96 hrs


title: PC-3 with shRNA NUSAP #2 knockdown 96 hrs Rep 1


title: DU145 with shRNA NUSAP #2 knockdown 96 hrs Rep 1


title: DU145 with Scramble knockdown 96 hrs Rep3


title: PC-3 with Scramble knockdown 96 hrs Rep3

description:
Knockdown_NUSAP1_using_shRNA_1_for_96_hours_in_PC3_cells.txt
Knockdown_NUSAP1_using_shRNA_2_for_96_hours_in_PC3_cells.txt


title: PC-3 with shRNA NUSAP #1 knockdown 96 hrs Rep 3

description: Knockdown_NUSAP1_using_shRNA_1_for_96_hours_in_PC3_cells.txt

value: shRNA NUSAP #1 knockdown 96 hrs


title: PC-3 with shRNA NUSAP #1 knockdown 96 hrs Rep 2


title: MCF10A-AT1_gapmer_IGFL2-AS1 rep1

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_AC006262_R1

data_processing:
Remove adapter reads (Cutadapt v1.6). Trim low quality base calls from both ends,  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v23/24). Genes with very low expression (<5  counts) were removed from the analysis.
Differential gene expression was calculated by using the DESeq2 version 1.8.1 package in R 3.2.0.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the normalized counts from the HTSeq-count quantification and DESeq2 analysis.

growth_protocol: MCF10A and MCF10AT1 cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10CA1a cells were grown in DMEM: F12 (Hyclone-SH30271) + 5% (v/v) horse serum (Gibco #16050) +Pen/Strep (Life Technologies) and  Glutamine (Life Technologies)  .

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701).
Barcoded libraries (Illumina TruSeq) wereloaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: MCF10A-AT1 cells were seeded at 2.5x105 cells per well in a 6-well plate. Cells were transfected with 10 nM negative control A GapmeR or GapmeR targeting IGFL2-AS1 using RNAiMAX (Invitrogen). 48 hours post-transfection, cells were washed twice with phosphate buffered saline (PBS) and stored at -80C in TRIzol.

value: breast

value: H-Ras transformed luminal ductal cells

value: fibrocystic disease

value: IGFL2-AS1 knockdown


title: MCF10A-AT1_gapmer_IGFL2-AS1 rep2

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_AC006262_R2


title: MCF10A-AT1_gapmer_control rep3

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_NS_R3

value: control


title: MCF10A-AT1_gapmer_IGFL2-AS1 rep3

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_AC006262_R3


title: PC-3 with shRNA NUSAP #1 knockdown 72 hrs Rep 3

description: Knockdown_NUSAP1_using_shRNA_1_for_72_hours_in_PC3_cells.txt

value: with shRNA NUSAP #1 knockdown 72 hrs


title: PC-3 with shRNA NUSAP #1 knockdown 72 hrs Rep 1

description:
Knockdown_NUSAP1_using_shRNA_1_for_72_hours_in_PC3_cells.txt
Knockdown_NUSAP1_using_shRNA_2_for_72_hours_in_PC3_cells.txt


title: PC-3 with shRNA NUSAP #1 knockdown 72 hrs Rep 2


title: PC-3 with Scramble knockdown 96 hrs Rep1


title: PC-3 with shRNA NUSAP #2 knockdown 72 hrs Rep 2

description: Knockdown_NUSAP1_using_shRNA_2_for_72_hours_in_PC3_cells.txt

value: with shRNA NUSAP #2 knockdown 72 hrs


title: MCF10A-AT1_gapmer_control rep2

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_NS_R2


title: PC-3 with shRNA NUSAP #1 knockdown 96 hrs Rep 1


title: PC-3 with Scramble knockdown 72 hrs Rep2

value: scramble knockdown 72 hrs


title: MCF10A-AT1_gapmer_control rep1

description:
mammary gland/breast epithelial cell
MCF10A-AT1_gapmer_IGFL2-AS1_Normalized_Counts.txt
MCF10A-AT1_NS_R1


title: PC-3 with Scramble knockdown 72 hrs Rep3


title: PC-3 with EGFP overexpression Rep 3

description: Over_expression_NUSAP1_in_PC3_cells_96_hours.txt

value: EGFP overexpression


title: PC-3 with Scramble knockdown 72 hrs Rep1


title: PC-3 with shRNA NUSAP #2 knockdown 72 hrs Rep 1


title: PC-3 with shRNA NUSAP #2 knockdown 72 hrs Rep 3


title: PC-3 with EGFP overexpression Rep 2


title: MCF10A-CA1_RNA-Seq rep3

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-CA1_R3


title: MCF10A-CA1_RNA-Seq rep2

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-CA1_R2


title: PC-3 with EGFP overexpression Rep 1


title: PC-3 with NUSAP1 overexpression Rep 3

value: NUSAP1 overexpression


title: PC-3 with NUSAP1 overexpression Rep 2


title: PC-3 with NUSAP1 overexpression Rep 1


title: PC-3 with Scramble knockdown 96 hrs Rep2

value: Scramble knockdown 96 hrs


title: MCF10A-CA1_RNA-Seq rep1

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-CA1_R1


title: MCF10A-AT1_RNA-Seq rep3

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-AT1_R3


title: MCF10A-AT1_RNA-Seq rep2

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-AT1_R2


title: MCF10A-AT1_RNA-Seq rep1

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a-AT1_R1


title: MCF10A_RNA-Seq rep3

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a_R3

value: basal epithelial, non-tumorigenic

value: ATCC CRL-10317


title: MCF10A_RNA-Seq rep2

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a_R2


title: MCF10A_RNA-Seq rep1

description:
mammary gland/breast epithelial cell
DESeq2_MCF10A_progression_normalized_counts.txt
MCF10a_R1


title: Set2-ChIPseq

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

data_processing:
Paired-end 50 bp reads were aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 2.2.3) (Langmead and Salzberg, 2012). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. The BEDTools toolset (Quinlan and Hall, 2010) was used to obtain coverage tracks that were subsequently imported into R/Bioconductor where further processing of the data was carried out. Normalization between IP and Input was done using the signal extraction scaling (SES) factor obtained with the estimateScaleFactor function from deepTools (Ramirez et al., 2014) with options: –l 100 –n 100000 and the median fragment size (-f) estimated from the data (around 200 bp). ChIP enrichments were obtained by dividing SES-normalized IP intensities by the corresponding input intensities: log2(IP/Input).
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: For each ChIP-seq experiment SES normalized log2(IP/Input) signals (Ramirez et al., 2014) are provided as processed data tracks in .bw (bigwig) format. Signals from replicates (if available) were averaged.

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: Yeast strains were grown in 600 mL YPD medium to mid-log phase (OD600, ~ 0.8).

extract_protocol:
Cells were collected by centrifugation, washed with 1 × TBS (20 mM Tris-HCL at pH 7.5, 150 mM NaCl) and twice with lysis buffer (50 mM HEPES-KOH at pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% Na deoxycholate, 0.1% SDS). Cell pellets were resuspended in 2 mL lysis buffer and lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Chromatin was washed with FA lysis buffer and solubilized via sonication with a Covaris S220 instrument (COVARIS, INC.) to yield an average DNA fragment size of 200 bp as determined on an Agilent 2200 TapeStation instrument (see below). This was achieved by sonicating the sample for 18 minutes using the following parameters: Peak Incident Power (W): 140; Duty Factor: 5%; Cycles per Burst: 200. 30 µL and 50 µL of the washed and fragmented chromatin samples were saved as input materials and for control of the average chromatin fragment size, respectively. The remaining chromatin sample was immunoprecipitated with 100 μL antibody-coated and prewashed magnetic Dynabeads® Protein G (life technologies) at 4 °C for 3 hr on a turning wheel. Immunoprecipitated chromatin was washed 5 times with ChIP wash buffer (100 mM Tris-HCl at pH 7.5, 500 mM LiCl, 1% NP-40, 1% Na deoxycholate) and one time with TE buffer (10 mM Tris-HCl at pH 7.5, 1 mM EDTA). Immunoprecipitated chromatin was eluted for 10 minutes at 70 °C in the presence of ChIP elution buffer (100 mM Sodium bicarbonate, 1% SDS). Eluted immunoprecipitated chromatin as well as input material and material for control of the average chromatin fragment size were incubated with 10 µL RNase A (10 mg/mL) at 37 °C for 30 minutes and subsequently subjected to Proteinase K (20 µL of 20 mg/mL Proteinase K, Bioline, BIO-37084) digestion at 37 °C for 2 hr and reversal of crosslinks (at 65 °C over night). DNA of the IP, mock IP, input, and fragment size control samples was purified with the QIAquick MinElute PCR Purification Kit (Qiagen) according to the manufacturers’ instructions. Samples used for determining the average chromatin fragment size were analyzed on an Agilent 2200 TapeStation instrument. DNA concentration of the IP and Input samples was determined with Qubit 1.0, dsDNA HS. Before preparing libraries for Illumina sequencing, IP and input samples were analysed via qRT-PCR on 4 housekeeping genes to access quality of sample DNA.
To prepare libraries of ChIP samples, 1–10 ng of IP or Input DNA were used for sequencing library preparation according to the manufacturer's recommendations using the ThruPLEX® DNA-seq Kit. Libraries were qualified on an Agilent 2200 TapeStation instrument and quantified with Qubit 1.0. Libraries were pooled and sequenced on an Illumina HiSeq 2500 sequencer.

treatment_protocol: Cell cultures were treated with formaldehyde (1%, Sigma F1635) for 20 minutes at 20°C. Crosslinking was quenched with 75 mL of 3 M glycine for 5 minutes at 20°C.

tag: strain

tag: variation

value: TAP

value: IgG

tag: method

value: ChIP-Seq


title: DD1618

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Library strategy: Hi-C
Standard Illumina Sequencing Pipeline
Hi-C Processing: HiCUP (Wingett S, Ewels P, Furlan-Magaril M et al. HiCUP: pipeline for mapping and processing Hi-C data (doi: 10.12688)
QDNAseq package with default parameters an 100kb bin size
Genome_build: Human: GRCh37;Mouse: NCBIM37
Supplementary_files_format_and_content: Hi-C interaction files lists interacting restriction fragments

source_name: Emanuel syndrome patient-derived lymphoblastoid cell line

growth_protocol: The transformed mouse cell line was grown in Dulbecco's modified eagle medium (DMEM) with 10% fetal calf serum (FCS) and 1% Penicillin/Streptomycin supplemented with puromycin. Human lymphoblastoid cell lines (FY1199 and DD1618 - European Collection of Cell Cultures (ECACC)) were grown in RPMI-1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin/Streptomycin. Tumors were received from Prof. V. Peter Collins (Department of Pathology, Addenbrooke’s Hospital, Cambridge, UK), with accompanying full ethical approval, as fresh frozen pieces consisting of between 75% and 90% tumor content, as determined by the pathologist. Approximately 160 mg of frozen tumor was finely chopped before being fixed and taken through the Hi-C protocol.

extract_protocol: As descirbed in: Nagano, T., et al. Comparison of Hi-C results using in-solution versus in-nucleus ligation. Genome biology 16, 175 (2015).

tag: cell line


title: Set2-Input

tag: chip antibody


title: Rtf1-ChIPseq


title: AA86

data_processing:
Library strategy: QDNAseq
Standard Illumina Sequencing Pipeline
Hi-C Processing: HiCUP (Wingett S, Ewels P, Furlan-Magaril M et al. HiCUP: pipeline for mapping and processing Hi-C data (doi: 10.12688)
QDNAseq package with default parameters an 100kb bin size
Genome_build: Human: GRCh37;Mouse: NCBIM37
Supplementary_files_format_and_content: Hi-C interaction files lists interacting restriction fragments

source_name: Anaplastic astrocytoma clinical tumour sample

extract_protocol: DNA was extracted from tumor tissue using the Qiagen QIAamp DNA Micro Kit, according to manufacturer’s instructions. Sequencing libraries were then prepared according to Scheinin, I., et al. Genome research 24, 2022-2032 (2014).

tag: tissue


title: Rtf1-Input


title: H3K79me3-ChIPseq

value: no tag

value: anti-Histone H3 (tri methyl K4) (Abcam, ab8580)


title: GB180

source_name: Glioblastoma clinical tumour sample

value: Glioblastoma clinical tumour sample


title: Set1-ChIPseq


title: FY1199

source_name: Lymphoblastoid cell line


title: H3K36me3-ChIPseq


title: Set1-Input


title: GB183


title: GB182


title: VGAT_anterior_cell_52

source_name: preopic area neuron

tag: mouse line abbreviation

tag: cre driver

tag: reporter

value: SADB-rEIAV-tloop-DIO-nls-YFP

tag: brain region

value: preoptic area

tag: dissection

value: anterior

tag: input material

value: single cell

tag: tdtomato labeling

tag: yfp labeling

value: Y

tag: passes qc checks

tag: animal id


title: H3K4me3-Input


title: H3K4me3-ChIPseq


title: GM07017

source_name: Human cell line control


title: VGAT_anterior_cell_51


title: VGAT_anterior_cell_50


title: GB238


title: GB176


title: VGAT_anterior_cell_49


title: VGAT_anterior_cell_48


title: Dot1-Input


title: VGAT_anterior_cell_47


title: H3K79me3-Input


title: H3K36me3-Input


title: VGAT_anterior_cell_46


title: VGAT_anterior_cell_45


title: Ctk1-Input


title: VGAT_anterior_cell_44


title: VGAT_anterior_cell_42


title: VGAT_anterior_cell_43


title: VGAT_anterior_cell_40


title: Bur1-ChIPseq


title: VGAT_anterior_cell_38


title: VGAT_anterior_cell_36


title: VGAT_anterior_cell_34


title: VGAT_anterior_cell_35


title: VGAT_anterior_cell_33


title: Spt6-Rep2-PAR-CLIP

data_processing:
Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina’s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner STAR (version 2.5.2b; options: --outFilterMultimapNmax 1, --outFilterMismatchNmax 1, --scoreDelOpen -10000, --scoreInsOpen -10000, --alignSJoverhangMin 10000, --alignSJstitchMismatchNmax 0 0 0 0). The resulting SAM files are then converted into BAM and PileUp files using SAMTools.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: For each factor PAR-CLIP crosslinked sites (p-values < 0.005) are provided in tab delimited text files (CLsites_Rpb1normalized_occupancies.table). For each crosslinked site the following is specified: chromosome, position, observed number of T-to-C transitions (m), number of reads covering the position (r), p-value, strand, and Rpb1 normalized RNA-binding occupancies (occ). To obtain these normalized occupancies, (m) was divided by the number of Rpb1 PAR-CLIP reads (Baejen et al., 2017) at that position. Finally, we set the maximal occupancy to the 95% quantile of all occupancies.

growth_protocol: Cells expressing the TAP-tagged protein were grown at 30 °C and 160 rpm. PAR-CLIP experiments were carried out in CSM minimal medium (Formedium) supplemented with 10 mg/l uracil, 100 µM 4-thiouracil and 2 % glucose.

extract_protocol:
Cells were lysed by bead beating and the lysate was sonicated in a Covaris S220 system. Immunoprecipitation was performed at 4 °C with rabbit IgG-conjugated Protein G magnetic Dynabeads.
For 3′ adaptor ligation, beads were resuspended in 1× T4 RNA ligase buffer (NEB) containing 10 U/µL T4 RNA ligase 2 (KQ) (NEB, M0373), 3′ adaptor [5 μM] (5′ rApp-TGGAATTCTCGGGTGCCAAGG-3ddC 3′, IDT), 1 U/µL RNase OUT, and 15% (w/v) PEG 8000. The bead suspension was incubated for 18 hr at 16°C and 600 rpm. Beads were washed in PNK buffer to remove unligated adapters. For 5′ adaptor ligation, beads were resuspended in 1× T4 RNA ligase buffer (NEB) containing 2 U/µL T4 RNA ligase 1 (NEB), 10 μM 5′ adaptor (5′ 5InvddT-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-OH 3′, IDT), 1 mM ATP, 1 U/µL RNase OUT, 5% (v/v) DMSO, and 10% (w/v) PEG 8000. The suspension was incubated for 4 hr at 24 °C and 600 rpm. Beads were washed twice in PNK buffer, and twice in proteinase K buffer (50 mM Tris-HCl pH 7.5, 6.25 mM EDTA, 75 mM NaCl). Beads were boiled twice at 95 °C for 5 minutes in proteinase K buffer with 1% SDS and eluted RNA-protein complexes were treated with 1.5 mg/mL proteinase K (NEB) for 2 hr at 55 °C. RNA was recovered by acidic phenol/chloroform extraction followed by ethanol precipitation supported by addition of 0.5 µL GlycoBlue (Invitrogen) and 100 μM RT primer (5′ HO-CCTTGGCACCCGAGAATTCCA-OH 3′). Reverse transcription was performed for 1 hr at 44 °C using SuperScript III RTase. For PCR amplification, NEXTflex barcode primer and universal primer and phusion HF master mix (NEB) were added.

treatment_protocol: 900 µM 4-thiouracil were added and cells were grown further for 4 h before they were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm.

tag: elongation factor

value: PAR-CLIP


title: VGAT_anterior_cell_26


title: Spt6-Rep1-PAR-CLIP


title: Dot1-ChIPseq

tag: strain


title: Dot1-Rep2-PAR-CLIP


title: Dot1-Rep1-PAR-CLIP


title: VGAT_anterior_cell_23


title: VGAT_anterior_cell_24


title: VGAT_anterior_cell_25


title: VGAT_anterior_cell_22


title: Ctk1-ChIPseq

tag: variation


title: Bur1-Input

tag: method


title: TFIIB-Rep2-PAR-CLIP

value: TFIIB


title: VGAT_anterior_cell_41


title: VGAT_anterior_cell_37


title: VGAT_anterior_cell_39


title: Set2-Rep2-PAR-CLIP


title: TFIIB-Rep1-PAR-CLIP


title: Set1-Rep2-PAR-CLIP


title: VGAT_anterior_cell_21


title: VGAT_anterior_cell_18


title: VGAT_anterior_cell_16


title: VGAT_anterior_cell_20


title: Set2-Rep1-PAR-CLIP


title: VGAT_anterior_cell_14


title: VGAT_anterior_cell_19


title: Set1-Rep1-PAR-CLIP


title: VGAT_anterior_cell_15


title: EKLF

source_name: Transformed cell line (EKLF-/-)

tag: cell line

value: EKLF


title: SATB1_total_rep3

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: SATB1 ChIP-seq of total thymocytes

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase

source_name: total thymocyte

growth_protocol: Thymus and peripheral lymphoid organ (Spleen/Lymph node) were derived from 4-6 wk old mice.

extract_protocol:
Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with anti-SATB1 antibody (Abcam, ab70001) that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified.
Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: total thymocyte

tag: antibody


title: VGAT_anterior_cell_13

tag: mouse line abbreviation


title: Rtf1-Rep3-PAR-CLIP


title: VGAT_anterior_cell_12

tag: cre driver


title: Rtf1-Rep2-PAR-CLIP


title: SATB1_input_rep2

description: Control SATB1 ChIP-seq of total thymocytes

value: input


title: Rtf1-Rep1-PAR-CLIP


title: SATB1_total_rep2

description: SATB1 ChIP-seq of total thymocytes


title: VGAT_anterior_cell_17

tag: reporter


title: VGAT_anterior_cell_10

tag: brain region


title: Paf1-Rep2-PAR-CLIP


title: SATB1_total_rep1

description: SATB1 ChIP-seq of total thymocytes


title: VGAT_anterior_cell_11

tag: dissection


title: VGAT_anterior_cell_8

tag: input material


title: SATB1_input_rep1

description: Control of SATB1 ChIP-seq of total thymocytes


title: VGAT_anterior_cell_9

tag: tdtomato labeling


title: Leo1-Rep3-PAR-CLIP


title: Paf1-Rep1-PAR-CLIP


title: SATB1_peripheral

description: SATB1 ChIP-seq of peripheral CD4+ T cell

source_name: peripheral CD4 T cell

value: peripheral CD4 T cell


title: SATB1_CD4

description: SATB1 ChIP-seq of CD4 SP thymocytes

source_name: CD4 thymocyte

value: CD4 thymocyte


title: Leo1-Rep1-PAR-CLIP


title: Leo1-Rep2-PAR-CLIP


title: Ctr9-Rep2-PAR-CLIP


title: VGAT_anterior_cell_7

tag: yfp labeling


title: WT3_mRNA

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

institute: Max Planck Institute for Molecular Biomedicine

description: mRNA

data_processing:
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed  using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and counts generated using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: Count table showing the raw counts of ribosome profiling and RNAseq data for detected GENCODE v24_knownCanonical transcipts (available from the UCSC table browser for hg38)

source_name: HAP-1 wild-type_RNA-seq

growth_protocol: Wild type and EEF1AKMT4-deficient HAP-1 cells were cultured  in IMDM GlutaMAX™, 10 % FBS and 100 U/ml penicillin-streptomycin.

extract_protocol:
RNASeq libraries were prepared from cells lysed similar to ribosome profiling samples. RNA was isolated from cleared lysates by addition of 1 % SDS (w/v) and 5 min incubation at 65 °C with intermittent vortexing followed by three rounds of extraction using 10:1 acid-phenol pH 4.3 and bromochloropropane.
Total RNA was precipitated and 5 µg used for library generation with the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions. Libraries were sequenced on an Illumina HiScanSQ generating 50 nt single-end reads.

tag: commercial name

value: Horizon Genomics, HAP1

tag: genotype

value: wildtype


title: VGAT_anterior_cell_5

tag: passes qc checks

tag: animal id


title: VGAT_anterior_cell_4


title: WT2_mRNA

description: mRNA


title: VGAT_anterior_cell_3


title: VGAT_anterior_cell_6


title: iKO-SC treated without doxycycline replicate 2

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs.

source_name: testes

extract_protocol:
Total RNA from SSCs was isolated by TRIzol. The RNA libraries were constructed by Illumina library preparation protocols. High-throughput sequencing was performed on HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: iKO-SC-1 and iKO-SC-2 were cultured on laminin-coated dishes overnight and then treated with or without 10 μg/ml doxycycline for two days.

tag: strain

value: DBA/C57 F1

tag: treatment

value: without doxycycline

tag: gender

value: male

tag: development stage

value: wild type


title: Cdc73-Rep3-PAR-CLIP

tag: elongation factor

tag: method


title: SATB1_DP

description: SATB1 ChIP-seq of DP thymocytes

source_name: DP thymocyte

tag: cell type

value: DP thymocyte

tag: antibody


title: Ctr9-Rep1-PAR-CLIP


title: WT1_mRNA

description: mRNA

tag: cell line


title: VGAT_anterior_cell_2

data_processing:
Adapter sequences were clipped from 100  or 75 base-pair single-end reads in FASTQ format using the ea-utils application fastq-mcf with settings -C 200000 to filter against Nextera adapter sequences.
Trimmed reads were aligned to GRCm38 (mm10) using the RefSeq annotation gff file downloaded on 6/1/2013. Transcriptome alignment files in BAM format were generated with RSEM v1.2.4 and Bowtie v1.1.0 using the program rsem-calculate-expression with settings --keep-intermediate-files --bowtie-chunkmbs 2000 --output-genome-bam --bowtie-e 500 --bowtie-m 100.
Reads that did not map to the RefSeq annotations were aligned to ERCC sequences, tdTomato sequence, and nls-YFP-WPRE sequence using Bowtie v1.1.0 with settings -S --chunkmbs 2000.
Genome_build: mm10
Supplementary_files_format_and_content: CSV: Comma-separated tables of data values; Columns are samples and Rows are genes or ERCC/tdTomato. Column names correspond to sample Titles; Row names correspond to RefSeq Gene Symbols, ERCC symbols, or tdTomato.

extract_protocol:
Individual adult male mice (P47-66) were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in fresh ice-cold artificial cerebrospinal fluid (ACSF). The brain was sectioned on a vibratome (Leica VT1000S) on ice, and each slice (300-400 µm) was immediately transferred to an ACSF bath at room temperature. After the brain slicing is complete (not more than 15 minutes), individual slices of interest were transferred to a small Petri dish containing bubbled room temperature ACSF. The regions of interest were microdissected under a fluorescence dissecting microscope. The dissected tissue pieces were transferred to a microcentrifuge tube and treated with 1 mg/ml pronase in carbogen-bubbled ACSF for 70 minutes at room temperature without mixing in a closed tube. After incubation, with the tissue pieces sitting at the bottom of the tube, the pronase solution was pipetted out of the tube and exchanged with cold ACSF containing 1% fetal bovine serum. The tissue pieces were dissociated into single cells by gentle trituration through Pasteur pipettes with polished tips of 600, 300, and 150-µm diameter. Single cells were isolated by FACS into individual wells of 96-well plates or 8-well PCR strips containing 2.275 µl of Dilution Buffer (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936), 0.125 µl RNase inhibitor (SMARTer kit), and 0.1 µl of 1:1,000,000 diluted RNA spike-in RNAs (ERCC RNA Spike-In Mix 1, Life Technologies Cat#4456740). Sorting was performed on a BD FACSAriaII SORP using a 130um nozzle, a sheath pressure of 10psi, and in the single cell sorting mode. To exclude dead cells, DAPI (DAPI*2HCl, Life Technologies Cat#D1306) was added to the single cell suspension to the final concentration of 2 ng/ml. FACS populations were chosen to select cells with low DAPI and high YFP fluorescence (for SADB-rEIAV-tloop-DIO-nls-YFP injected animals) or  tdTomato (tdT) fluorescence (for Chat-IRES-Cre;Ai14 animals). Sorted cells were frozen immediately on dry ice and stored at -80°C.
We used the SMARTer kit from Clontech (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936)  to reverse transcribe single cell RNA, and amplify the cDNA for 19 PCR cycles. To stabilize the RNA after quickly thawing the cells on ice, we immediately added to each sample an additional 0.125 µl of RNase inhibitor mixed with SMART CDS Primer II A. All steps downstream were carried out according to the manufacturer’s instructions. Each amplification experiment included a set of controls: 10 pg cortex RNA (isolated from Rbp4-Cre;Ai14, P57 male) as positive control for amplification, ERCC-only control to demonstrate the absence of RNases throughout the sorting process, and water-only control, to control for specificity of amplification/absence of contamination. cDNA concentration was quantified using Agilent Bioanalyzer High Sensitivity DNA chips. For most samples, 1 ng of amplified cDNA was used as input to make sequencing libraries with Nextera XT DNA kit (Illumina Cat#FC-131-1096).  We stopped the procedure after PCR clean-up and did not perform library normalization or library pooling. Individual libraries were quantified using Agilent Bioanalyzer DNA 7500 chips. In order to assess sample quality and adjust the concentrations of libraries for multiplexing on HiSeq or NextSeq. Libraries were sequenced on Illumina HiSeq single end 100-bp or NextSeq single end 75-bp.

tag: mouse line abbreviation

tag: cre driver

tag: reporter

value: SADB-rEIAV-tloop-DIO-nls-YFP

tag: brain region

value: preoptic area

tag: dissection

value: anterior


title: Cdc73-Rep2-PAR-CLIP

value: PAR-CLIP


title: VGAT_anterior_cell_1

tag: input material

value: single cell

tag: tdtomato labeling

tag: yfp labeling

value: Y


title: KO3_mRNA

description: mRNA

source_name: HAP-1 EEF1AKMT4_RNA-seq

tag: commercial name

value: Horizon Genomics, HZGHC000530c015

tag: genotype

value: EEF1AKMT4 KO


title: iKO-SC treated without doxycycline replicate 1

tag: strain

tag: treatment

tag: gender


title: iKO-SC treated with doxycycline replicate 2

value: with doxycycline

tag: development stage


title: Cdc73-Rep1-PAR-CLIP

tag: elongation factor

tag: method


title: Ctk2-Rep2-PAR-CLIP


title: GAD_anterior_cell_11

tag: passes qc checks

tag: animal id


title: iKO-SC treated with doxycycline replicate 1


title: GAD_anterior_cell_10

tag: mouse line abbreviation

tag: cre driver


title: Ctk2-Rep1-PAR-CLIP


title: Ctk1-Rep2-PAR-CLIP


title: Ctk1-Rep1-PAR-CLIP


title: GAD_anterior_cell_7

tag: reporter

tag: brain region


title: GAD_anterior_cell_9

tag: dissection

tag: input material


title: KO3_RPF

description: mRNA - ribosome footprints

data_processing:
Library strategy: ribosome profiling
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed  using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and counts generated using a custom script.
Genome_build: hg38
Supplementary_files_format_and_content: Count table showing the raw counts of ribosome profiling and RNAseq data for detected GENCODE v24_knownCanonical transcipts (available from the UCSC table browser for hg38)

source_name: HAP-1 EEF1AKMT4_ribosomal profiling

extract_protocol:
For ribosome profiling, lysates were subsequently treated with 250 U RNase I (Ambion) for 10 min at 22 °C and shaking at 1400 rpm. The digestion was stopped by addition of 100 U SUPERase In RNase inhibitor (Ambion). Ribosomes were separated on a 10-50 % (w/v) sucrose density gradient in 50 mM Tris pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT, 100 µg/ml CHX for 3 h at 35 000 rpm and 4 °C in a TH-641 rotor (Thermo Scientific). Gradients were fractionated at 0.75 ml/min with continuous monitoring of OD254 on a density gradient fractionator (Isco) coupled to a SYR-101 syringe pump (Brandel). SDS was added immediately to 1 % and 400 µl fractions were flash-frozen in liquid nitrogen and stored at -80 °C until further processing. Monosome fractions were pooled, RNA isolated and separated on 15 % polyacrylamide gels (8 M urea, 1 x TBE). Ribosome footprints were excised between 28 nucleotide (nt) and 32 nt RNA size markers. Sequencing libraries from ribosome footprints were generated essentially as described (27), except for ligation to a preadenylated 3’-adapter (5’ rAppNNNNCTGTAGGCACCATCAAT/3ddC/ 3’) in a reaction containing 200 000 U T4 RNA ligase 2 (truncated, NEB), 25 % PEG 8000 and 10 U SUPERase In RNase inhibitor for 4 h at 22 °C. The first four bases of the 3’-adapter were randomized to minimize ligation bias (28).
Sequencing libraries from ribosome footprints were generated essentially as described (27), except for ligation to a preadenylated 3’-adapter (5’ rAppNNNNCTGTAGGCACCATCAAT/3ddC/ 3’) in a reaction containing 200 000 U T4 RNA ligase 2 (truncated, NEB), 25 % PEG 8000 and 10 U SUPERase In RNase inhibitor for 4 h at 22 °C. The first four bases of the 3’-adapter were randomized to minimize ligation bias (28).

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide (CHX) for 1 min, washed with ice cold PBS containing 100 µg/ml CHX and subsequently lysed in lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 100 µg/ml CHX).

value: Horizon Genomics, HZGHC000530c012

tag: cell line


title: Bur2-Rep2-PAR-CLIP


title: GAD_anterior_cell_8

tag: tdtomato labeling

tag: yfp labeling


title: KO2_RPF

description: mRNA - ribosome footprints

tag: commercial name

value: Horizon Genomics, HZGHC000530c011

tag: genotype


title: KO1_RPF

description: mRNA - ribosome footprints

extract_protocol:
For ribosome profiling, lysates were subsequently treated with 250 U RNase I (Ambion) for 10 min at 22 °C and shaking at 1400 rpm. The digestion was stopped by addition of 100 U SUPERase In RNase inhibitor (Ambion). Ribosomes were separated on a 10-50 % (w/v) sucrose density gradient in 50 mM Tris pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT, 100 µg/ml CHX for 3 h at 35 000 rpm and 4 °C in a TH-641 rotor (Thermo Scientific). Gradients were fractionated at 0.75 ml/min with continuous monitoring of OD254 on a density gradient fractionator (Isco) coupled to a SYR-101 syringe pump (Brandel). SDS was added immediately to 1 % and 400 µl fractions were flash-frozen in liquid nitrogen and stored at -80 °C until further processing. Monosome fractions were pooled, RNA isolated and separated on 15 % polyacrylamide gels (8 M urea, 1 x TBE). Ribosome footprints were excised between 28 nucleotide (nt) and 32 nt RNA size markers.
Sequencing libraries from ribosome footprints were generated essentially as described (27), except for ligation to a preadenylated 3’-adapter (5’ rAppNNNNCTGTAGGCACCATCAAT/3ddC/ 3’) in a reaction containing 200 000 U T4 RNA ligase 2 (truncated, NEB), 25 % PEG 8000 and 10 U SUPERase In RNase inhibitor for 4 h at 22 °C. The first four bases of the 3’-adapter were randomized to minimize ligation bias (28).

value: Horizon Genomics, HZGHC000530c010


title: GAD_anterior_cell_5


title: GAD_anterior_cell_6


title: Bur1-Rep3-PAR-CLIP


title: Bur2-Rep1-PAR-CLIP


title: KO2_mRNA

description: mRNA

value: Horizon Genomics, HZGHC000530c014


title: Bur1-Rep2-PAR-CLIP


title: GAD_anterior_cell_4


title: KO1_mRNA

description: mRNA

value: Horizon Genomics, HZGHC000530c013


title: GAD_anterior_cell_3


title: Bur1-Rep1-PAR-CLIP


title: GAD_anterior_cell_2