title: TOM6

source_name: tdTomato-positive multiciliated cells 6

value: tdTomato-positive multiciliated cells


title: TOM2

status: Public on Sep 19 2017

type: SRA

city: Boston

first: Matthew

middle: Robert

last: Jones

state: MA

address: 72 East Concord Street

department: Medicine

country: USA

institute: Boston University School of Medicine

library_source: transcriptomic

data_processing:
Quality assessment using Fastqc and subsequent trimming with Cutadapt 1.7.1
STAR 2.4.2a alignment to the GRCm38.p4 genome with appended tdTomato marker cassette
Indexed bam files were converted to raw counts using HTseq with Gencode M10 gene annotation reference
DESeq2 was used for normalization, statistical comparisons and expression differences
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: tdTomato-positive multiciliated cells 2

extract_protocol:
Lungs from Miwi2tdTomato mice were enzymatically digested to achieve a single cell suspension which was then subject to FACS using CD45-EpCAM+tdTomato-/+ gates.
Total RNA was isolated using Trizol, cleaned with Qiagen RNAeasy mini kit, amplified with Ovation RNA-Seq System V2, and used to prepare TruSeq Nano DNA libraries.

tag: cell type

tag: strain

tag: individual

value: Mouse 1

tag: tissue

value: lung


title: ScR 1

status: Public on Sep 20 2017

city: yantai

first: cheng-gang

last: ren

state: shandong

address: 17 Chunhui Road, Laishan District

country: China

institute: Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, China

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample:
1. Clean data were mapped back onto the assembled transcriptome
2. Readcount for each gene was obtained from the mapping results
Genome_build: De novo transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sesbania cannabina

source_name: root

extract_protocol:
Total RNA from the samples was isolated in two biological replicates using TRIzol (Invitrogen, USA) following the manufacture’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: root

tag: developmental stage

value: 30 days old seedling

tag: genotype

value: wild type


title: R-R1

city: Madison

first: Charu

last: Mehta

state: Wisconsin

address: 1111 Highland Avenue 4028 WIMR

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

description: Barcode: GTGCTT

data_processing:
mRNAseq reads are trimmed and filtered to remove contaminant and low quality bases prior to the analysis using skewer version 0.1.123:  /skewer -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -k 15 -l 25 -t 8 -o trimmed_fq/O-R1 /O-R1_AGTGAG_L001_R1_001.fastq.gz
Align to genome ENSEMBL_GRCm37.67 using STAR version 2.5:  STAR-2.5/STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /genomes/Mus_musculus/ENSEMBL_GRCm37.67/STARIndex --genomeFastaFiles /genomes/Mus_musculus/ENSEMBL_GRCm37.67/genome.fa --sjdbGTFfile genomes/Mus_musculus/ENSEMBL_GRCm37.67/annotation/genes.gtf --sjdbOverhang 100
Reads assignment and expression estimation using RSEM version 1.2.31:  /rsem-calculate-expression  --bam alignments/O-R1_aligned_transcriptome.bam --keep-intermediate-files --no-bam-output -p 8 /genomes/Mus_musculus/ENSEMBL_GRCm37.67/RSEMIndex/genome tmp/rsem_estimate/O-R1
Compare differential expression (DE) between conditions/treatment using DESeq2 version :  https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf
Genome_build: mm9 (GRCm37.67)
Supplementary_files_format_and_content: R1_bowtie.RSEM.DESeq2_gene.diffexpr.txt

source_name: Mouse Fetal Liver

extract_protocol:
E14.5 fetal livers were removed, CD71medTer119- (R1) erythroid precursor cells were sorted, and RNA was harvested using Trizol reagent and purified using RNAeasy MiniElute Spin column (Qiagen, Cat. 1026497). NuGEN Ovation Single Cell RNA-Seq System (Part no. 0342HV lot #1512556) was used with 10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NuGEN Ovation protocols

value: Mouse Fetal Liver

value: erythroid precursor cells

tag: age


title: O-R1

description: Barcode: AGTGAG


title: TOM1

source_name: tdTomato-negative multiciliated cells 1

value: tdTomato-negative multiciliated cells


title: i-R1

description: Barcode: GCACTA


title: Individual 2

city: Arcachon

first: Anthony

last: Bertucci

address: Place du Dr Peyneau

country: France

institute: University of Bordeaux

data_processing:
Reads have been aligned to contigs with bwa (version 0.7.12) with standard parameters. Resulting sam files were sorted and indexed with samtools (version 1.1) with standard parameters. Expression counts were generated from the bam files with samtools.
Filtered reads were assembled using DRAP version 1.7 and the Trinity assembler (www.sigenae.org/drap)
Genome_build: Margaritifera_assembly.fas
Supplementary_files_format_and_content: raw counts : comma-separated csv file including count values for each sample / assembly : fasta file

organism: Margaritifera margaritifera

extract_protocol:
SV Total RNA isolation system kit (Promega) according to manufacturer’s instructions
TruSeq RNA Library Prep Kit v2

tag: location

value: upstream

tag: year

tag: age class

value: old

value: kidney


title: F-R1

description: Barcode: GTCGTA


title: d-R1

description: Barcode: ACCTCA


title: TOM4

source_name: tdTomato-positive multiciliated cells 4

value: Mouse 2


title: h-R1

description: Barcode: AAGCCT


title: E804

city: Cleveland

first: David

last: Buchner

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were aligned to the genome using TopHat2
Reads not aligned to the C57BL/6J genome were aligned to the A/J genome from The Sanger Institute using Seqnature
HT-Seq was used to count the number of reads for each gene feature
EdgeR was used to analyze gene expression
Genome_build: mm10

source_name: Liver

growth_protocol: Five-week-old mice were fasted overnight

extract_protocol:
Tissue was homogenized using the TissueLyser II (Qiagen) and RNA was isolated using the PureLink RNA mini kit (ThermoFisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were anesthetized with isoflurane prior to euthanasia


title: E805


title: E781


title: E760


title: E748


title: E776


title: E96


title: E761


title: E752


title: E747


title: E745


title: E744


title: E736


title: E733


title: E732


title: E731


title: E742


title: E73


title: E727


title: E719


title: E713


title: E710


title: E708


title: E707


title: E802


title: E774


title: E70


title: E701


title: E694


title: E675


title: E688


title: E677


title: E674


title: E679


title: E689


title: E691


title: E678


title: E672


title: E653


title: E67


title: E642


title: E623


title: E608


title: E614


title: E60


title: E596


title: E597


title: E584


title: E586


title: E575


title: E566


title: E559


title: E662


title: E663


title: E530


title: E54


title: E565


title: E540


title: E647


title: E548


title: E518


title: E630


title: E514


title: E527


title: E513


title: E506


title: E501


title: E520


title: E485


title: E511


title: E50


title: E496


title: E472


title: E45


title: E459


title: E571


title: E457


title: E464


title: E460


title: E448


title: E422


title: E437


title: E44


title: E421


title: E441


title: E411


title: E413


title: E419


title: E407


title: E395


title: E412


title: E401


title: E379


title: E373


title: E375


title: Thy1_PRC1dKO_rep1

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the mm10 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
Genome_build: mm10

source_name: Thy1+ spermatogonia

extract_protocol: Total RNA was purified using an RNeasy micro kit (Qiagen) according to the manual provided. RNA quality and quantity were checked using Bioanalyzer (Agilent) and Qubit (Life technologies), respectively. The initial amplification step was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. Libraries were then created by Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced with Illumina HiSeq 2500.

value: Thy1+ spermatogonia

value: testis

tag: biowardrobe ides


title: E374


title: E369


title: S4_heads_RNAseq

city: Stanford

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Drive, Alway M-341

department: Genetics

institute: Stanford University

description: rRNA-depleted RNA

data_processing:
gene expression: fastx_trimmer was used to trim the 75th and 76th base from reads.
gene expression: Trimmed reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations, using the parameters "-N 5 --segment-mismatches 3 --read-edit-dist 5".
gene expression: Read counts were obtained using featureCounts from the Subread package.
gene expression: DESeq2 was used to obtain gene expression levels.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: gene expression: The processed data files contain gene expression counts for each sample that served as input for DESeq2.  The tab-delimited columns are formatted as: gene name, gene expression count.
RNA editing levels: fastx_trimmer was used to trim the 75th and 76th base from reads.
RNA editing levels: Trimmed reads were mapped to the dm3 genome in addition to 70bp of exonic sequence surrounding known splice junctions using BWA, with the default settings.
RNA editing levels: Duplicate reads were marked using Picard, and duplicate and unmapped reads were removed using Samtools, as well as reads with a mapping quality less than 10
RNA editing levels: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing levels: RNA editing levels were calculated as the number of 'G' reads divided by the number of 'A' and 'G' reads at each site, for bases that had a quality score of at least 20.
Supplementary_files_format_and_content: RNA editing levels: The processed data files contain editing levels for each Evolution Canyon fly line.  The tab-delimited columns are formatted as: chromosome, position, number of A reads, number of G reads, editing level.  Editing sites for which there was no coverage are not included.

organism: Drosophila melanogaster

source_name: Male heads

growth_protocol: For each sample, 5 heads or whole bodies were collected from 3-5 day old male adult flies that were raised at 25˚C.

extract_protocol:
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), and depleted of ribosomal RNA.
Libraries produced using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 76-bp cycles.

value: head


title: E366


title: E323


title: E361


title: E350


title: E349


title: E324


title: E32


title: E318


title: E290


title: E394


title: E297


title: E285


title: E271


title: E284


title: E310


title: E277


title: E387


title: E268


title: E224


title: E237


title: E241


title: E242


title: E260


title: E26


title: E22


title: E217


title: E210


title: E202


title: E188


title: E187


title: E215


title: E191


title: E181


title: E176


title: E317


title: E165


title: E270


title: E163


title: E16


title: E137


title: E153


title: E141


title: E136


title: E232


title: E138


title: E162


title: E146


title: E122


title: E131


title: E132


title: E116


title: E125


title: E124


title: E11


title: E2


title: E103


title: Y4

city: Jerusalem

first: Yiska

last: Weisblum

address: Kiryat Hadassah

country: Israel

institute: Hadassah Hebrew University Medical Center

data_processing:
Trimming the 51st position, then trimming the 3' end, using an in-house Perl script, with a quality threshold of 35.
Adapter sequences were removed using an in-house perl script allowing for up to 10% mismatches and requiring at least 6 bases overlap
The remaining reads were further filtered using the fastq_quality_filter program of the FASTX package (version 0.0.14) with a quality threshold of 30 in at least 95% of the read's positions.
The processed fastq files were mapped to the human genome GRCh37 using TopHat version 2.0.13 with Ensembl release 75 annotations. The following configuration was used: -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 20 --read-realign-edit-dist 4
Quantification, normalization and differential expression were done with the Cufflinks package (v2.2.1). Quantification was done with cuffquant, using the -b and -u parameters. Differential expression was calculated with cuffdiff, using default parameters.

organism: Homo sapiens

source_name: Decidua

extract_protocol:
Tissues were washed extensively, frozen and RNA was purified using M&N Nucleospin RNA purification kit according to the protocol.
RNA libraries were prepared for sequencing using standard Illumina TrueSeq protocols

value: Decidua

tag: infection

value: HCMV

tag: pool number

tag: time post infection


title: Y2


title: Y3

value: Mock


title: Y1


title: Apoe knock-out_Phagocytic_06

first: Oleg

last: Butovsky

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

description: KO 06 P

data_processing:
Transcripts were quantified by the BTL computational pipeline using Cuffquant version 2.2.1(Trapnell et al., 2012). The BTL’s internal QC pipeline utilizes Mm10 (UCSC Link) and GENCODE mouse genome (GRCm38), version 9 (Ensembl 84) annotations. Reads are demultiplexed on a third Illumina read, and then each sample’s sequences are aligned utilizing STAR v2.4.2a. Alignments are then processed using Picard v1.1073 tools to add read groups and other sequencing information via AddOrReplaceReadGroups, reorder the BAM file to the reference via ReorderSam, and mark duplicate sequences via MarkDuplicates. After this, the pipeline gathers summary metrics via the following Picard commands: CollectAlignmentSummaryMetrics, QualityScoreDistribution, CollectReadGCMetrics, MeanQualityByCycle, CollectInsertSizeMetrics. Genes are then quantified using RSEM v1.2.21 (Li, et. al) with the paired-end option. The data is then assessed for quality using RNA-SeQC (Deluca, et. al.). Raw counts were normalized using TMM normalization and then log2-transformed. Batch effects were corrected using removeBatchEffect from the R package limma (v. 3.28.21). Supplementary_files_format_and_content: FPKM and TPM values of gene expression from RNA-seq data in tab-delimited text format.
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: FACS sorted MG cells

extract_protocol:
Samples (1,000 FACS-sorted FCRLS+ microglia cells) were lysed in TCL buffer.
Smart-Seq2 libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform. cDNA libraries were generated from sorted cells using the Smart-seq2 protocol (Picelli et al., 2013). RNA sequencing was performed using Illumina NextSeq500 using a High Output v2 kit to generate 2 x 25 bp reads.

value: microglia

value: Apoe knock-out


title: Apoe knock-out_Phagocytic_08

description: KO 08 P


title: Apoe knock-out_Phagocytic_07

description: KO 07 P


title: Apoe knock-out_Phagocytic_05

description: KO 05 P


title: Apoe knock-out_Phagocytic_04

description: KO 04 P


title: Apoe knock-out_Phagocytic_09

description: KO 09 P


title: Apoe knock-out_Phagocytic_03

description: KO 03 P


title: Apoe knock-out_Phagocytic_02

description: KO 02 P


title: Apoe knock-out_NonPhagocytic_09

description: KO 09 NP


title: Apoe knock-out_NonPhagocytic_10

description: KO 10 NP


title: Apoe knock-out_Phagocytic_01

description: KO 01 P


title: Apoe knock-out_NonPhagocytic_08

description: KO 08 NP


title: E117


title: Apoe knock-out_NonPhagocytic_07

description: KO 07 NP


title: Apoe knock-out_NonPhagocytic_06

description: KO 06 NP


title: Apoe knock-out_NonPhagocytic_04

description: KO 04 NP


title: Apoe knock-out_NonPhagocytic_05

description: KO 05 NP


title: WT_Phagocytic_08

description: WT 08 P

value: WT


title: WT_Phagocytic_06

description: WT 06 P


title: Apoe knock-out_NonPhagocytic_01

description: KO 01 NP


title: WT_Phagocytic_09

description: WT 09 P


title: Apoe knock-out_NonPhagocytic_03

description: KO 03 NP


title: WT_Phagocytic_10

description: WT 10 P


title: WT_Phagocytic_07

description: WT 07 P


title: WT_Phagocytic_05

description: WT 05 P


title: WT_Phagocytic_03

description: WT 03 P


title: WT_Phagocytic_02

description: WT 02 P


title: WT_Phagocytic_01

description: WT 01 P


title: WT_NonPhagocytic_10

description: WT 10 NP


title: WT_NonPhagocytic_08

description: WT 08 NP


title: WT_NonPhagocytic_09

description: WT 09 NP


title: WT_Phagocytic_04

description: WT 04 P


title: WT_NonPhagocytic_06

description: WT 06 NP


title: WT_NonPhagocytic_05

description: WT 05 NP


title: WT_NonPhagocytic_03

description: WT 03 NP


title: WT_NonPhagocytic_04

description: WT 04 NP


title: WT_NonPhagocytic_02

description: WT 02 NP


title: WT_NonPhagocytic_07

description: WT 07 NP


title: WT_NonPhagocytic_01

description: WT 01 NP


title: APP-PS1_Clec7apositive_05


title: APP-PS1_Clec7apositive_06


title: APP-PS1_Clec7apositive_04


title: Apoe knock-out_NonPhagocytic_02

description: KO 02 NP


title: APP-PS1_Clec7apositive_02


title: APP-PS1_Clec7apositive_01


title: APP-PS1_Clec7apositive_03


title: APP-PS1_Clec7anegative_06


title: APP-PS1_Clec7anegative_05


title: APP-PS1_Clec7anegative_04


title: APP-PS1_Clec7anegative_03


title: APP-PS1_Clec7anegative_02


title: WT_Clec7anegative_04


title: WT_Clec7anegative_03


title: WT_Clec7anegative_02


title: SOD1:TREM2-Het (Male)-04

description: SOD1:TREM2-Het (Male)-04

tag: gender

value: Male


title: SOD1:TREM2-Het (Female)-01

description: SOD1:TREM2-Het (Female)-01

value: Female


title: SOD1:TREM2-Het (Male)-03

description: SOD1:TREM2-Het (Male)-03


title: SOD1:TREM2-KO (Female)-05

description: SOD1:TREM2-KO (Female)-05


title: WT_Clec7anegative_06


title: SOD1:TREM2-KO_(Male)-07


title: SOD1:TREM2-Het (Female)-02

description: SOD1:TREM2-Het (Female)-02


title: SOD1:TREM2-KO_(Male)-05


title: SOD1:TREM2-KO_(Male)-06


title: SOD1:TREM2-KO (Female)-02

description: SOD1:TREM2-KO (Female)-02


title: SOD1:TREM2-KO_(Male)-04


title: SOD1:TREM2-KO (Female)-01

description: SOD1:TREM2-KO (Female)-01


title: SOD1:TREM2-KO (Female)-04

description: SOD1:TREM2-KO (Female)-04


title: SOD1:TREM2-KO_(Male)-03


title: SOD1:TREM2-KO_(Male)-02


title: WT_Clec7anegative_05


title: APP-PS1_Clec7anegative_01


title: SOD1:TREM2-Het (Male)-02

description: SOD1:TREM2-Het (Male)-02


title: SOD1:TREM2-Het (Female)-04

description: SOD1:TREM2-Het (Female)-04


title: SOD1:TREM2-KO_(Male)-01


title: SOD1:TREM2-Het (Male)-01

description: SOD1:TREM2-Het (Male)-01


title: SOD1:TREM2-KO (Female)-03

description: SOD1:TREM2-KO (Female)-03


title: 2489_4XG_Vogels2

city: Berkeley

first: Areejit

last: Samal

address: 341A Koshland Hall

department: Plant & Microbial Biology

country: India

institute: UC Berkeley

data_processing:
Sequenced libraries were mapped to the current version of the Neurospora crassa OR74A genome (v12) using Tophat v2.0.5(Trapnell et al, 2009; Trapnell et al, 2012).
Transcript abundance was estimated in FPKM (fragments per kilobase of transcript per million mapped reads) using Cufflinks v2.0.2 (Trapnell et al, 2009; Trapnell et al, 2012) with options of upper quartile normalization and mapping against reference isoforms.
Differential expression analysis was conducted using Cuffdiff v2.0.2 (Trapnell et al, 2009; Trapnell et al, 2012). Genes with a multiple-hypothesis adjusted p-value below 0.05 and at least two-fold induction were determined to be significantly differentially expressed between conditions.
Genome_build: Neurospora crassa OR74A genome (v12)
Supplementary_files_format_and_content: Tab-separated values containing Cufflinks output

molecule: polyA RNA

organism: Neurospora crassa

source_name: whole fungus_2% xyloglucan

growth_protocol: Neurospora crassa strains were pre-grown for 24 hrs on 3 mL agar slants of Vogel's minimal media (VMM) with 2% sucrose, at 30°C under dark conditions. The slants were placed under constant light at 25°C to stimulate conidia production. For flask cultures, conidia were collected and inoculated (10^6 conidia/mL) into 100 mL liquid VMM (2% sucrose) at 25°C, under constant light and shaking (200 rpm).

extract_protocol:
After 4 hrs in the new carbon source, the mycelia were harvested over a filter, flash frozen in liquid nitrogen and stored at −80°C. Total RNA was extracted using Phenol Chlorophorm, ethanol precipitated, and DNAsed and cleaned on a Qiagen column.
Single end libraries were prepared for RNA sequencing (RNA-seq) using an Illumina kit (RS-100-0801) following standard protocols as described in Coradetti et al. (Coradetti et al, 2012). The cDNA libraries were sequenced on the Illumina HiSeq 2000 platform at the Vincent J. Coates Genomic Sequencing Laboratory, University of California, Berkeley.

treatment_protocol: First, using shake-flasks (200 rpm), Neurospora crassa cultures were pre-grown from conidia for 16 hrs in 100 mL of Vogels Minimal Medium (VMM) with 2% sucrose. Next, the mycelia were passed over a Whatman glass microfiber filter and washed three times with VMM without a carbon source (NoC). The mycelial mass was then transferred to new shake flasks with 100 mL of VMM containing a specific carbon source 2% xyloglucan (P-XYGLN, Megazyme) or 2% mannan (P-MANCB, Megazyme) or 2% mixed-linkage-glucan (P-BGBM, Megazyme) or 2% starch.

value: Neurospora crassa OR74A (FGSC2489)

value: wildtype

value: mycelia


title: 2489_4XG_Vogels3


title: SOD1:TREM2-Het (Female)-03

description: SOD1:TREM2-Het (Female)-03


title: 2489_4STARCH_Vogels3

source_name: whole fungus_2% starch


title: 2489_4STARCH_Vogels1

source_name: whole fungus_2% mixed-linkage-glucan


title: 2489_4STARCH_Vogels2


title: 2489_4MLG_Vogels3


title: RNA_Control_rep2

city: Research Triangle Park

first: Pishun

state: NC

address: 111 T.W. Alexander Drive

department: ESCBL

institute: National Institute of Environmental Health Sciences

description: Gene expression  4 days after transfection

data_processing:
Aligned with TopHat2 version 2.0.4 with the following parameters: --b2-sensitive --no-coverage-search -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)

source_name: mouse ES cell line E14Tg2A

growth_protocol: Embryonic stem cells were cultured at 37°C, 5% CO2,  in DMEM (Sigma) with 10% foetal bovine serum and leukemia inhibitory factor (LIF).

extract_protocol:
Cells were harvested and total RNA was extracted by Thermo RNA kit
The sequencing library was generated by Truseq RNA sample preparation kit according to the instruction

treatment_protocol: Cells were infected with lenti-viral based shNT (control) or shRif1(Rif1 KD), cells were harvested  4 days after infection.

value: mouse embryonic stem cell line

tag: cell line


title: RNA_Control_rep1


title: RNA_Rif1KD_rep1


title: 2489_4MLG_Vogels2


title: 2489_4MAN_Vogels3

source_name: whole fungus_2% mannan


title: 2489_4MLG_Vogels1


title: 2489_4MAN_Vogels2


title: ChIP_Rif1KD_H3K27me3

description: ChIP-Seq in shRif1 treated cells

library_source: genomic

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -M 1 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph: coverage normalized to reads per 10 million aligned reads

molecule: genomic DNA

extract_protocol:
Treated cells were fixed, harvested, and lysed, then submitted to sonication. The sonicated DNA was incubated with specific beads-conjugated antibody overnight. Then the beads were washed, and DNA was eluted, and quantified.
The sequencing library was generatedusing Nextera XT DNA preparation Kit

treatment_protocol: For ChIP-seq of Rif1, we first introduce HA tag at N-terminal endogenous Rif1 using CRISPR/Cas9 system. For ChIP-seq of histone modification, cells were infected with lenti-viral based shNT (control) or shRif1(Rif1 KD), cells were harvested  4 days after infection.


title: ChIP_Rif1KD_H3K9me3

description: ChIP-Seq in shRif1 treated cells


title: ChIP_Rif1KD_H3

description: ChIP-Seq in shRif1 treated cells


title: ChIP_Rif1KD_Input

description: ChIP-Seq in shRif1 treated cells


title: Recr D12_2

city: Denver

first: Kara

last: Mould

state: CO

address: 1400 Jackson Street

institute: National Jewish Health

description: recruited alveolar macrophages, 12 days post LPS

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 4.0.2.
Sequence reads of at least 30 nt length were mapped to the mm10 release of the mouse genome using STAR (version 2.4.0a) with splice site data from the Ensembl annotation as downloaded from UCSC on July 29, 2013.
Reads mapping unambiguously to each gene in the Ensembl annotation were quantified using the htseq-count program from the HTSeq package (version 0.6.0) in the “intersection-nonempty” mode.
Statistical comparisons of the gene expression between the cell genotypes were performed with the DESeq2 package version 1.4.5 for the R statistical software version 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text table (derived from htseq-count)

source_name: Alveolar macrophages

growth_protocol: C57B/6 mice, ages 8 to 14 weeks were used in the study.

extract_protocol:
Alveolar macrophages were isolated using bronchoalveolar lavage with phosphate-buffered saline and separated via fluorescence activated cell sorting using previously validated cell surface markers.
Isolated total RNA was processed for next-generation sequencing (NGS) library construction as developed in the NJH Genomics Facility for analysis with a Life Technologies (Carlsbad, CA, USA) Ion Proton NGS platform. A modified Kapa Biosystems (Wilmington, MA, USA) KAPA Stranded mRNA-Seq kit for whole transcriptome libraries was used to primarily target all polyA RNA. Briefly, library construction started from isolation of total RNA species, followed by mRNA (poly-A) isolation, 1st and 2nd strand cDNA synthesis, adaptor ligation, amplification, and bead templating. Once validated, the libraries were sequenced as barcoded-pooled samples on a P1 Ion Proton chip, as routinely performed by the NJH Genomics Facility

treatment_protocol: Mice were treated with 20 nanograms lipopolysacchride in 50 microliters sterile phosphate-buffered saline via intratracheal instillation.

value: Alveolar macrophages

tag: treatment

value: Day 12 post lipopolysacchride

tag: cell surface markers


title: Recr D12_1

tag: cell type

tag: strain


title: 2489_4XG_Vogels1

tag: tissue


title: Recr D12_3


title: ChIP_Rif1KD_H3K27ac

description: ChIP-Seq in shRif1 treated cells


title: 2489_4MAN_Vogels1


title: BD030

city: Pittsburgh

first: Mark

middle: Jay

last: Shlomchik

state: PA

address: W1052 Biomedical Science Tower 200 Lothrop St

department: Department of Immunology

institute: University of Pittsburgh

description: Barcode: GTTTCG

data_processing:
RNA-Seq reads were aligned to hg19 with Tophat with default parameters
HTSeq was used to obtain gene read counts.
DESeq2 was used to normalize the read counts for library size difference correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: blood

growth_protocol: Human tissues were obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved research protocol and MTA with LiveOnNY, the organ procurement organization for the New York metropolitan area. All donors were free of chronic disease and cancer, were Hepatitis B, C, and HIV-negative. Tissues were collected after the donor organs were flushed with cold preservation solution and clinical procurement process was completed. Isolation of tissues from organ donors does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals. Demographic and clinical data were extracted from summaries prepared by LiveOnNY. For isolation of blood from living volunteers, blood was drawn via venipuncture from consented volunteers, as approved by the Columbia University IRB. A list of donors and individuals from whom samples were obtained for this study is presented in Table S4.

extract_protocol:
CD3+CD4+ and CD3+CD8+ TEM (CD45RA-CCR7-) cells were sorted into CD69+ and CD69- subsets based on the gating strategy in Fig. S1, from spleen and lung tissue of three individual donors (D226, D233, D250, see Table S4), and CD4+ and CD8+ TEM cells were sorted from peripheral blood using the BD-influx sorter. RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen), and RNA concentration and quality was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies). For the majority of samples, >400ng of total RNA was submitted for sequencing
standard Truseq with poly-A pulldown

treatment_protocol: Tissue samples were maintained in cold saline and brought to the laboratory within 2-4hrs of organ procurement. Spleen and lung samples were processed using enzymatic and mechanical digestion resulting in high yields of live leukocytes, as described previously (Sathaliyawala et al., 2013; Thome et al., 2014). Lymphocytes were isolated from blood samples using centrifugation through lymphocyte separation medium (Corning) for recover of mononuclear cells.

value: blood

tag: tcell type

tag: cd69 status

value: Negative


title: RNA_Rif1KD_rep2


title: MeDIP_5mC_Rif1KD

description: MeDIP-seq in shRif1(Rif1 KD) treated cells

extract_protocol:
Genomic DNA was extracted and then submitted to sonication. The sonicated DNA was incubated with 5mC antibody-conjugated beads overnight. Then the beads were washed, and DNA was eluted, and quantified.
The sequencing library was generated following the guide NEXTflex™ kits for DNA library prep for Illumina® sequencing


title: BD029

description: Barcode: GTGGCC


title: Recr D9_3

description: recruited alveolar macrophages, 9 days post LPS

value: Day 9 post lipopolysacchride


title: Recr D9_1


title: ChIP_Rif1KD_H3K4me3

description: ChIP-Seq in shRif1 treated cells


title: MeDIP_5mC_Control

description: MeDIP-seq in shNT(control) treated cells


title: BD028

description: Barcode: GTGAAA


title: ChIP_Control_H3

description: ChIP-Seq in shNT treated cells


title: BD027

description: Barcode: GTCCGC


title: Recr D6_3

description: recruited alveolar macrophages, 6 days post LPS

value: Day 6 post lipopolysacchride


title: ChIP_Control_H3K9me3

description: ChIP-Seq in shNT treated cells


title: BD026

description: Barcode: CCGTCC


title: Recr D6_1


title: ChIP_Control_H3K27me3

description: ChIP-Seq in shNT treated cells


title: Recr D6_2


title: ChIP_Control_H3K27ac

description: ChIP-Seq in shNT treated cells


title: BD024

description: Barcode: CTTGTA

source_name: lung

value: lung

value: Positive


title: ChIP_Control_H3K4me3

description: ChIP-Seq in shNT treated cells


title: Recr D3_3

description: recruited alveolar macrophages, 3 days post LPS

value: Day 3 post lipopolysacchride


title: ChIP_WT_Input

description: ChIP-Seq in HA-tag Rif1 cells

source_name: HA-tag introduced by homologous recombination at the gene encoding Rif1 in mouse ES cell line E14Tg2A


title: BD022


title: BD023

description: Barcode: GGCTAC


title: Recr D3_1


title: ChIP_WT_Rif1

description: ChIP-Seq in HA-tag Rif1 cells


title: Res D12_3

description: resident alveolar macrophages, 12 days post LPS


title: Recr D9_2


title: ChIP_Control_Input

description: ChIP-Seq in shNT treated cells


title: BD021

description: Barcode: TAGCTT


title: ATAC_Rif1KD

description: library strategy: ATAC-seq

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -M 1 --best --strata
Open chromatin signal was generated from coverage of the first 9 nt of aligned reads
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph: open chromatin signal normalized to reads per 10 million aligned reads

extract_protocol:
50,000 cells were collected, washed with PBS and resuspended in 50ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1%(v/v%) Igepal CA-630). Permeabilized cells were resuspended in 50 ul Transposase reaction (1X Tagmentation buffer, 1.0-1.5 ul Tn5 transposase enzyme (Illumina)) and incubated for 30min at 37°C. Subsequent steps  were performed as described in PMID: 24097267
Transposed DNA was subjected to several(8-9) round of amplification with  primer pairs (Oligonucleotide sequences are available in PMID: 24097267). Libraries were next purified using  Ampure XP magnetic beads.


title: Res D12_2


title: ATAC_Control

description: library strategy: ATAC-seq


title: BD019

description: Barcode: ACTTGA

source_name: spleen

value: spleen


title: BD017

description: Barcode: GCCAAT


title: Res D12_1


title: BD018

description: Barcode: CAGATC


title: BD025

description: Barcode: ATTCCT


title: Res D9_2

description: resident alveolar macrophages, 9 days post LPS


title: Res D9_3


title: BD016

description: Barcode: CCGTCC


title: Res D9_1


title: Res D6_3

description: resident alveolar macrophages, 6 days post LPS


title: BD015

description: Barcode: ATGTCA


title: Res D6_2


title: Recr D3_2


title: BD014

description: Barcode: AGTTCC


title: WT_Clec7anegative_01

value: microglia

tag: genotype

value: WT


title: Res D6_1


title: BD010

description: Barcode: TAGCTT


title: BD013

description: Barcode: AGTCAA


title: BD012

description: Barcode: CTTGTA


title: Res D3_3

description: resident alveolar macrophages, 3 days post LPS


title: Res D3_2


title: Res D0_2

description: resident alveolar macrophages, untreated

value: No treatment control


title: BD011

description: Barcode: GGCTAC


title: Res D3_1


title: BD009

description: Barcode: ATTCCT


title: Res D0_3


title: BD020

description: Barcode: GATCAG


title: Spt8_5min

city: Seattle

first: Sebastian

last: Gruenberg

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
SGY98: ade2Δ::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 SPT8-3FLAGMNase(83-231)-kanMX6
Spt8 ChEC-seq in synthetic medium for 5 min after CaCl2 addition.
Barcode: TTAGGC

data_processing:
We used Novoalign 2.08.03 (http://www.novocraft.com) with options -a -r Random to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random.
We extracted properly paired reads.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
We normalized base pair counts by dividing by the total number of fragment ends mapped, and then multiplying by the total number of mapped base pairs (processed data files .wig). Generation and normalization of tracks was performed with https://github.com/zentnerlab/chec-seq/blob/master/pairs_single_end_sizes.pl.
HOMER (http://homer.salk.edu) (Heinz et al, 2010) was used to generate reads per million (RPM)- normalized average plots.
Genome_build: sacCer3 from UCSC
Supplementary_files_format_and_content: wig

organism: Saccharomyces cerevisiae

source_name: Spt8 ChEC-seq

growth_protocol: For each ChEC experiment, a 50 mL culture was grown to an OD600 of 0.5-0.7 at 30C.

extract_protocol: Cells were pelleted at 3,000 x g and washed three times with 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), centrifuging as above between washes. Cells were resuspended in 600 µL Buffer A containing 0.1% digitonin and permeabilized at 30C for 5 min. CaCl2 was added to 2 mM and ChEC digests were performed at 30C. 5 min after CaCl2 addition, a 100 µL aliquot of the digest was transferred to a tube containing 100 µL 2X stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA) and 1% SDS. Protein was then was digested with 80 µg proteinase K at 55C for 30 m. Nucleic acids were extracted with an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 2.5 volumes 100% ethanol and 30 µg Glycogen (Roche). Pellets were washed once with 1 mL 100% ethanol, dried, and resuspended in 30 µL 0.1X TE buffer, pH 8.0. RNA was digested with 10 µg RNase A at 37C for 20 m. Prior to generating sequencing libraries, ChEC DNA was subjected to size-selection using Ampure XP beads (ThermoFischer). A beads:sample ratio of 2.5:1 was used and the unbound fraction, containing small DNA fragments, was extracted to remove RNase and precipitated as above, and used for library preparation. Sequencing libraries were constructed as described (PMID 27797823).

value: SGY98:ade2{delta}::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SPT8-3FLAGMNase(83-231)-kanMX6


title: BD004

description: Barcode: TGACCA


title: Spt7_5min

description:
SGY96; ade2Δ::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 SPT7-3FLAGMNase(83-231)-kanMX6
Spt7 ChEC-seq in synthetic medium for 5 min after CaCl2 addition.
Barcode: ACAGTG

source_name: Spt7 ChEC-seq

value: SGY96; ade2{delta}::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SPT7-3FLAGMNase(83-231)-kanMX6


title: BD008

description: Barcode: ACTTGA


title: Res D0_1

value: No treatment  control


title: BD006

description: Barcode: GCCAAT


title: Spt3_5min

description:
SGY95; ade2Δ::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 SPT3-3FLAGMNase(83-231)-kanMX6
Spt3 ChEC-seq in synthetic medium for 5 min after CaCl2 addition.
Barcode: ATCACG

source_name: Spt3 ChEC-seq

value: SGY95; ade2{delta}::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 SPT3-3FLAGMNase(83-231)-kanMX6


title: BD001

description: Barcode: ATCACG


title: BD002

description: Barcode: CGATGT


title: HLe110_H3K36me3_mm10

city: Montreal

first: Stephen

last: Nemec

state: Quebec

address: 110 Av. des Pins Ouest

country: Canada

institute: IRCM

description: single-end reads

data_processing:
Single-end reads were mapped using Bowtie version 1.1.2, with 5-6 bp trimmed from the 5' end of the read, e.g. "bowtie -t -p 8 --trim5 5 --trim3 0 --best mm10 -S --chunkmbs 1024 HLe110_H3K27ac_rep2_mm10.fastq HLe110_H3K27ac_rep2_mm10.sam"
Paired-end reads were mapped using Bowtie2 version 2.2.6 in paired-end mode, e.g. "bowtie2 -t -p 12 --fr -I 0 -X 1000 -x /gs/project/feb-684-aa/BIF/genomes/BOWTIE2_INDEXES/mm10 -1 R1.fastq -2 R2.fastq -S HLe115_Pitx1_mm10PE.sam"
Peak calling was performed on Pitx1 and Tbx5 datasets with MACS version 2.1.1.20160309 in paired-end mode, using otherwise default parameters for mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated with HOMER with read counts normalized per 10000000 reads (default). Summit files are in BED format, with the score in the 5th column indicating the -LOG10(qvalue) as output by MACS. The HLe115Pitx1_mm10PE_summits_Mrep2.txt file contains three additional columns that indicate the corresponding peak score in the Pitx1 ChIPseq dataset in Menke et al., 2013, and the distance from the summit to either edge of the corresponding peak in that dataset.

growth_protocol: Timed breedings of wild type CD1 were collected at the indicated embryonic stages.

extract_protocol:
Tissue was fixed with 1% formaldehyde, nuclei were isolated, genomic DNA was sheared by sonication, and protein:DNA complexes were pulled down with the indicated antibodies.
Illumina

tag: developmental stage

value: hindlimb

value: wild type

tag: chip antibody

value: Kimura CMA333/13C9


title: HLe110_Input_mm10

description: paired-end reads


title: HLe110_H3K9me3_mm10

description: single-end reads


title: HLe110_H3K27me3_mm10

description: single-end reads

value: Diagenode C15410196


title: HLe110_H3K27ac_mm10

description: single-end reads

value: CST #9733BC


title: HLe110_H3K4me3_mm10

description: single-end reads

value: CST #9751BF


title: BD003

description: Barcode: TTAGGC

value: Negative


title: HLe110_H3K4me1_mm10

description: single-end reads

value: CST #5326BF


title: FLe105_H3K27ac_mm10

description: single-end reads

value: forelimb


title: Ubp8_5min

description:
SGY99; ade2Δ::hisG his3Δ200 leu2Δ0 lys2Δ0 met15Δ0 trp1Δ63 ura3Δ0 UBP8-3FLAGMNase(83-231)-kanMX6
Ubp8 ChEC-seq in synthetic medium for 5 min after CaCl2 addition.
Barcode: CAGATC

source_name: Ubp8 ChEC-seq

value: SGY99; ade2{delta}::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 UBP8-3FLAGMNase(83-231)-kanMX6


title: FLe105_H3K36me3_mm10

description: single-end reads


title: FLe105_Input_mm10

description: single-end reads


title: FLe105_H3K27me3_mm10

description: single-end reads


title: FLe105_H3K4me1_mm10

description: single-end reads


title: FLe105_H3K4me3_mm10

description: single-end reads


title: BD005

description: Barcode: ACAGTG

value: lung


title: BD007

description: Barcode: CAGATC


title: RNA-Seq DKI CD11b-CD27+

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: DKI CD11b-CD27+

data_processing:
Sequenced readsWere aligned to the mm9 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to bam format using samtools. MACSWas used to call peaks for ChIP-Seq data. RPKM model (reads per kilobase per million reads)Was used to normalize gene expression values for RNA-Seq data.
Genome_build: mm9

source_name: Spleen

growth_protocol: For ChIP-Seq, Splenic NK cells from 10WT and 13 Stat5 DKI miceWere purified (Miltenyi Biotec Inc.), expanded in vitroWith 20 ng/ml of human recombinant IL-15 (R&D Systems or BioLegend) for 10 days,With fresh rhIL-15 being added every two days, yielding 50-80 million of nearly 100% pure CD3-CD122+NK1.1+ cells. For RNA-Seq, librariesWere prepared using 150 ng of total RNA from bone marrow NK cells and splenic NK subpopulations.

extract_protocol:
For ChIP-Seq, and cross-linkedWith 1% formaldehyde (methanol-free, Pierce, Rockford, IL) at room temperature for 10 min. After sonication, fragmented chromatin equivalent to 10 million cellsWas immunoprecipitatedWith control rabbit IgG (Santa Cruz Biotechnology, Dallas TX) or anti-STAT5B (R&D systems) and Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). ChIP-Seq DNA librariesWere prepared using KAPA LTP Library Preparation Kit (Kapa Biosystems,Wilmington, MA) and indexed primers (BIOO Scientific, Austin, TX), and the librariesWere then sequenced. For RNA-Seq, KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems,Wilmington, MA), and each libraryWas indexed using barcoded primers (BIOO Scientific, Austin, TX). Barcoded PCR productsWere purified on 2% E-Gel, 250-400 bp fragmentsWere purified, quantified on Qbit (Invitrogen), mixed, and sequenced on an Illumina HiSeq2000 platform.
PCR productsWere barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform.

treatment_protocol: For ChIP-Seq, cellsWereWashed 3 timesWith medium, rested in complete RPMI-1640 mediumWithout IL-15 for 2 hr, not treated or treatedWith 40 ng/ml of IL-15 for 1 hr. For RNA-Seq, cellsWere either directly sorted from splenic NK subpopulations, orWithout orWith IL-15 for 2h, 6h or 24h.

tag: genotype/variation

value: DKI


title: RNA-Seq DKI CD11b+CD27+

description: DKI CD11b+CD27+


title: RNA-Seq DKI CD11b+CD27low

description: DKI CD11b+CD27low


title: RNA-SeqWT CD11b+CD27low

description: WT CD11b+CD27low

value: WT


title: RNA-SeqWT CD11b+CD27+

description: WT CD11b+CD27+


title: RNA-SeqWT CD11b-CD27+

description: WT CD11b-CD27+


title: FLe105_H3K9me3_mm10

description: single-end reads


title: RNA-Seq DKI +IL15 24h

description: DKI IL15 24h


title: RNA-Seq DKI +IL15 6h

description: DKI IL15 6h


title: FLe105_Input_Tbx5_mm10PE

description: paired-end reads


title: RNA-Seq DKI +IL15 2h

description: DKI IL15 2h


title: RNA-Seq DKI -IL15

description: DKI noIL15


title: RNA-SeqWT +IL15 6h

description: WT IL15 6h


title: RNA-SeqWT +IL15 2h

description: WT IL15 2h


title: HLe115_Pitx1_mm10PE

description: paired-end reads

value: homemade (960A)


title: HLe115_Input_mm10PE

description: paired-end reads


title: Nuclear_RNA_Control_SAM

city: Riverside

first: Mauricio

middle: A

last: Reynoso

address: 4126 Genomics Bldg

department: Botany and Plant Sciences

institute: University of California Riverside

description: Random primed libraries

data_processing:
Library strategy: Nuclear RNA-Seq and polyA RNA-Seq
Base calling and demultiplexing performed with Illumina CASAVA version 1.8. (UC Davis DNA Tech Core)
R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control.
The processed short reads were mapped to the Oryza sativa genome (Version IRGSP-1.0-30) using TopHat v2.1.1 (Trapnell et al., 2009) with command "tophat -p 8 -g 1 -i 50 -I 3000 -G Oryza_sativa.IRGSP-1.0.30.gff3".
Read count data in terms of RPKM (reads per kilobase per million) were calculated for exons on gene ( Genomic features exonsby).
Genome_build: Genome_build:  IRGSP-1.0 (http://plants.ensembl.org/Oryza_sativa/Info/Index?db=core)

molecule: nuclear RNA

organism: Oryza sativa Japonica Group

source_name: 3 w-old plants 1 cm shoot base

growth_protocol: Seeds were treated for two days in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote even germination. The seeds were then rinsed with distilled water and placed back at 28° C in dark for one day. The germinated seeds were then transferred to pots (15 cm diameter and 18 cm height) filled with Profile® Green GradesTM in a greenhouse at UC Riverside (28°C day / 20°C night under natural light conditions) during spring. The pots were placed in trays and watered with fresh water. After 13 days of growth, fertilized water (Peters® Excel: 21-5-20 at 100 ppm N) was used instead for 8 days.

extract_protocol:
Nuclei were purified from frozen and pulverized pOSH1:OsNTF1 tissue as described previously for Arabidopsis thaliana (Wang and Deal, 2015) with only minor modifications including use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh (Celltrics) to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB (this suspension is considered input of the purification), Twenty-five microliters of M-280 streptavidin-coated Dynabeads (~1.5 x 107 beads; Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated to allow capture of the nuclei in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 7 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 7 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube. For RNA extraction, the bead-bound nuclei mixture was placed on a 2 mL tube magnet for 4 min at 4° C to capture the nuclei, which were resuspended in 20 µl NPB before proceeding to the extraction.
Nuclear RNA library, pre-rRNA was degraded with probes that were hybridized with up to 1 µg RNA in a 6 μl reaction containing 0.1 μM of each probe and 1 μl of 5x hybridization buffer (0.5 M Tris-HCl [pH 7.0], 1 M NaCl). The probe concentration was scaled down proportionally for lower amounts of RNA. For denaturation and hybridization, the sample was heated to 95 °C for 2 min, cooled to 45 °C at 0.1 °C/s and incubated at 45 °C for 5 min. For RNase treatment, the hybridization reaction at 45 °C was  increased to 10 μl by adding 5 U of thermostable RNase H Hybridase (Epicentre) and 1 μl of Hybridase buffer (500 mM Tris-HCl [pH 7.4], 1 M NaCl, 200 mM MgCl2), and incubated at 45 °C for 30 min. To remove the DNA probes and degraded RNA from the samples, the sample was re-treated with Turbo DNase I (ThermoFisher Scientific) and cleaned up with Agencourt RNAClean XP beads (Beckman Coulter). RNA-seq libraries of pre-rRNA degraded nuclear were prepared as described by Townsley et al. (2014)

treatment_protocol: Transgenic Oryza sativa seeds (cv. Nipponbare) were treated for two days in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote even germination. The seeds were then rinsed with distilled water and placed back at 28° C in dark for one day. The germinated seeds were then transferred to pots (15 cm diameter and 18 cm height) filled with Profile® Green GradesTM in a greenhouse at UC Riverside (28°C day / 20°C night under natural light conditions) during spring. The pots were placed in trays and watered with fresh water. After 13 days of growth, fertilized water (Peters® Excel: 21-5-20 at 100 ppm N) was used instead for 8 days.

tag: cultivar

value: Nipponbare

tag: line

value: shoot base


title: ChIP-Seq DKI +IL15, anti-STAT5B

description: DKI IL15 STAT5B

tag: antibody

value: anti-STAT5B (R&D systems)


title: HLe115Pitx1_WT_run126_rep3

description:
mRNA enrichment, unstranded
processed data file: HLe115Pitx1_WT_vs_KO_GLMRobustDisp_edgeR.txt

data_processing:
Reads were mapped to mm10 using STAR (Dobin et al., 2013) with the following parameters: STAR --runThreadN 16 --genomeDir /GRCm38p87_STAR_index_sjdb49 --readFilesIn R1.fastq R2.fastq --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverLmax 0.04 --outFilterMatchNminOverLread 0.75 --outSAMtype BAM Unsorted
Transcript features were counted at the level of the gene using featureCounts (Liao et al., 2014) with the GRCm38p87 gene transfer format file.
Differential gene expression was assessed using edgeR, with robust dispersion estimates, likelihood ratio testing, and a generalized linear model to accommodate batch effects between replicates.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text containing edgeR differential gene expression output coupled to the counts-per-million figures for each replicate in the comparison

growth_protocol: Timed breedings of wild type CD1, Pitx1 wt (BalbC) and Pitx1 knockout, were collected at the indicated embryonic stages.

extract_protocol: Total RNA was extracted via silica gel spin-column purification for all samples.

value: hindlimb

value: BALB/c


title: ChIP-Seq IgG Control

description: IgG control

value: rabbit IgG (Santa Cruz)


title: ChIP-Seq DKI -IL15, anti-STAT5B

description: DKI Cont STAT5B


title: HLe115Pitx1_WT_run3982_rep1

description:
mRNA enrichment, stranded
processed data file: HLe115Pitx1_WT_vs_KO_GLMRobustDisp_edgeR.txt

value: wild type


title: FoxAa>Bra Rep3

city: Manhattan

first: Michael

last: Veeman

state: KS

address: 116 Ackert Hall

department: Division of Biology

institute: Kansas State University

data_processing:
base-calling by RTA (Real Time Analysis) v1.18.61
Sequenced reads were mapped to the Ciona KH2012 gene models using Tophat (v2.9.8b) with default parameters
Transcript abundances were calculated with Cuffquant (Cufflinks v2.2.1) with parameters default parameters
Normalized abundances and differential expression was quantitated wth Cuffdiff (Cufflinks v2.2.1)
Genome_build: KH2012 gene models
Supplementary_files_format_and_content: tab delimited txt file containing FPKM values for each treatment, as well as differential expression analysis

organism: Ciona intestinalis

source_name: whole embryo stage 19.5

growth_protocol: Ciona embryos grown at 21 degrees Celsius in artificial seawater

extract_protocol:
400 embryos were collected at Hotta stage 19.5 into RNA lysis buffer and stored at -80C until RNA purification.RNA was purified with the Zymogen Quick-RNA miniprep kit (R1054) and eluted in 50 ul elution buffer. Final purified RNA concentration was 52-60 ng/ul.
Libraries were constructed with the TruSeq stranded mRNA library kit (Illumina) using standard protocols. Libraries were quality checked with an Agilent Tapestation and quantified by qPCR.

treatment_protocol: Fluorescently labeled by electroporation of reporter construct into fertilized eggs

tag: reporter construct

value: FoxAa>Venus-Bra

value: Ciona intestinalis type A


title: HLe115Pitx1_KO_run126_rep3

value: Pitx1 null


title: FLe105_Tbx5_mm10PE

description: paired-end reads

value: homemade (NP1723)


title: HLe115Pitx1_KO_run3982_rep1


title: Nuclear_RNA_Control

description: Random primed libraries

source_name: 7 days-old seedling 1 cm roots tips

growth_protocol: Seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. After 2 days, germinated seedlings were passed to plates (12 cm x 12 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 5 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 μEm-2s-1)

extract_protocol:
Nuclei were purified from frozen and pulverized p35S:OsNTF2 tissue as described previously for Arabidopsis thaliana (Wang and Deal, 2015) with only minor modifications including use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh (Celltrics) to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB (this suspension is considered input of the purification), Twenty-five microliters of M-280 streptavidin-coated Dynabeads (~1.5 x 107 beads; Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated to allow capture of the nuclei in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 7 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 7 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube. For RNA extraction, the bead-bound nuclei mixture was placed on a 2 mL tube magnet for 4 min at 4° C to capture the nuclei, which were resuspended in 20 µl NPB before proceeding to the extraction.
For nuclear RNA libraries, rRNA was degraded with probes that were hybridized with up to 1 µg RNA in a 6 μl reaction containing 0.1 μM of each probe and 1 μl of 5x hybridization buffer (0.5 M Tris-HCl [pH 7.0], 1 M NaCl). The probe concentration was scaled down proportionally for lower amounts of RNA. For denaturation and hybridization, the sample was heated to 95 °C for 2 min, cooled to 45 °C at 0.1 °C/s and incubated at 45 °C for 5 min. For RNase treatment, the hybridization reaction at 45 °C was  increased to 10 μl by adding 5 U of thermostable RNase H Hybridase (Epicentre) and 1 μl of Hybridase buffer (500 mM Tris-HCl [pH 7.4], 1 M NaCl, 200 mM MgCl2), and incubated at 45 °C for 30 min. To remove the DNA probes and degraded RNA from the samples, the sample was re-treated with Turbo DNase I (ThermoFisher Scientific) and cleaned up with Agencourt RNAClean XP beads (Beckman Coulter). RNA-seq libraries of pre/rRNA degraded nuclear were prepared as described by Townsley et al. (2014)

treatment_protocol: Transgenic Oryza sativa cv. Nipponbare seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. For nuclei isolation, seedlings were grown on plates (12 cm x 12 cm) containing half-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 μEm-2s-1)

value: roots tip


title: ChIP-SeqWT +IL15, anti-STAT5B

description: WT IL15 STAT5B


title: HLe115Pitx1_WT_run3982_rep2


title: FoxAa>Bra Rep2


title: PolyA_RNA_Control

description: Random primed libraries

data_processing:
Library strategy: Nuclear RNA-Seq and polyA RNA-Seq
Base calling and demultiplexing performed with Illumina CASAVA version 1.8. (UC Davis DNA Tech Core)
R/Bioconductor (version 3.2.1) and FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were used in short read quality control and grep for filtering of oligo dT for PolyA RNA libraries.
The processed short reads were mapped to the Oryza sativa genome (Version IRGSP-1.0-30) using TopHat v2.1.1 (Trapnell et al., 2009) with command "tophat -p 8 -g 1 -i 50 -I 3000 -G Oryza_sativa.IRGSP-1.0.30.gff3".
Read count data in terms of RPKM (reads per kilobase per million) were calculated for exons on gene ( Genomic features exonsby).
Genome_build: Genome_build:  IRGSP-1.0 (http://plants.ensembl.org/Oryza_sativa/Info/Index?db=core)

growth_protocol: Seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. After 2 days, germinated seedlings were passed to plates (12 cm x 12 cm) containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 5 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 μEm-2s-1)

extract_protocol:
For cellular mRNA, p35S:HF-FLAG-OsRPL18 pulverized tissue was extracted in PEB and a S16 fraction was obtained as detailed by Mustroph et al. 2009). Total poly(A)+ RNA was extracted by direct capture of poly(A)+ RNA using a biotinylated oligo dT according to Townsley et al., 2014
RNA-seq libraries poly(A)+ selected total mRNA were prepared as described by Townsley et al. (2014)

treatment_protocol: Transgenic Oryza sativa cv. Nipponbare seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min and then rinsed with sterile distilled water. For nuclei isolation, seedlings were grown on plates (12 cm x 12 cm) containing full-strength Murashige and Skoog standard medium (MS) agar (1% w/v) and 1% w/v sucrose, during 7 days in a growth chamber (16 h day / 8 h night;  at 28°C/25°C day/night; 110 μEm-2s-1)

value: p35S:HF-FLAG-OsRPL18 (Zhao et al., 2016)


title: HLe110Pitx1_WT_run3412_L_rep3

description:
ribosomal depletion, stranded
processed data file: HLe110Pitx1_WT_vs_KO_GLMRobustDisp_edgeR.txt


title: FoxAa>Bra Rep1


title: RNA-SeqWT +IL15 24h

description: WT IL15 24h


title: HLe115Pitx1_KO_run3982_rep2


title: RNA-SeqWT -IL15

description: WT noIL15


title: control Rep3 (FoxAa)

value: Bra>GFP


title: HLe110Pitx1_KO_run3412_L_rep3


title: ChIP-SeqWT -IL15, anti-STAT5B

description: WT Cont STAT5B


title: control Rep1 (FoxAa)


title: control Rep2 (Cytochalasin)

data_processing:
base-calling by RTA (Real Time Analysis)  v1.18.64
Sequenced reads were mapped to the Ciona KH2012 gene models using Tophat (v2.9.8b) with default parameters
Transcript abundances were calculated with Cuffquant (Cufflinks v2.2.1) with parameters default parameters
Normalized abundances and differential expression was quantitated wth Cuffdiff (Cufflinks v2.2.1)
Genome_build: KH2012 gene models
Supplementary_files_format_and_content: tab delimited txt file containing FPKM values for each treatment, as well as differential expression analysis

treatment_protocol: Dechorionated embryos were treated with DMSO control or 10 micromolar Cytochalasin B starting at 64 cell stage (3.75hpf) and then harvested at stage 19.5

value: DMSO


title: control Rep2 (FoxAa)


title: Cytochalasin Rep2

value: 10 micromolar Cytochalasin


title: HLe110Pitx1_WT_run3982_rep1


title: Cytochalasin Rep3


title: HLe110Pitx1_KO_run3982_rep2


title: control Rep1 (Cytochalasin)


title: HLe110_run3982_rep1

description:
ribosomal depletion, stranded
processed data file: FLe105_vs_HLe110_GLMRobustDisp_edgeR.txt


title: Cytochalasin Rep1


title: Emb2 Rep1

data_processing:
base-calling by RTA (Real Time Analysis) v1.17.21.3
Sequenced reads were mapped to the Ciona KH2012 gene models using Tophat (v2.9.8b) with default parameters
Transcript abundances were calculated with Cuffquant (Cufflinks v2.2.1) with parameters default parameters
Normalized abundances and differential expression was quantitated wth Cuffdiff (Cufflinks v2.2.1)
Genome_build: KH2012 gene models
Supplementary_files_format_and_content: tab delimited txt file containing FPKM values for each stage/cell type, as well as differential expression analysis

source_name: dissociated embryo

extract_protocol:
Cell sorting was performed using a Biorad S. For each timepoint, an unelectroporated cell sample was first analyzed to determine the levels of background autofluorescence and gates on forward scatter and GFP fluorescence were conservatively selected to enrich for single cells with or without strong GFP signal. The electroporated sample was then sorted directly into RNA lysis buffer (Zymogen Quick RNA miniprep kit R1054). For GFP positive notochord enriched cells, 2000-15000 cell were purified into 500 ul buffer, while 100,000 GFP negative (notochord depleted) cells were simultaneously sorted into 2 mL of lysis buffer. Samples were stored at -80C until RNA purification.RNA was purified with the Zymogen Quick-RNA miniprep kit (R1054) and eluted in 50 ul elution buffer.10-60 ng of RNA per sample was treated with DNAse (Roche) and concentrated to 10 ul with the Zymogen Clean and Concentrator kit (R1015). Final purified RNA concentration was 0.5 – 4.0 ng/ul.
Amplifed cDNA was prepared using the NuGEN Ovation RNA-Seq System V2 (7102) .  2.5 ul of purified RNA was used in half-reactions following their standard protocol. cDNA samples were fragmented with the Covaris S220 Ultrasonicator using the recommended settings to obtain average fragment length of 300bp and the NEBNext DNA Library Prep Master Mix set for Illumina from New England BioLabs (NEB ) was used for library construction. Obtained libraries were checked with the Agilent 2100 Bioanalyzer

treatment_protocol: Fluorescently labeled by electroporation of notochord reporter construct Bra>GFP into fertilized eggs

tag: hotta stage

value: Stage 19/20

value: notochord-depleted

tag: harvest time

value: 7.5 hpf

tag: type

value: type A


title: HLe110Pitx1_KO_run3982_rep1

value: hindlimb


title: Noto2 Rep2

value: notochord-enriched


title: Emb2 Rep3


title: Emb2 Rep2


title: control Rep3 (Cytochalasin)

tag: treatment


title: Emb1 Rep3

value: Stage 16

tag: cell type


title: HLe110_rep3

tag: strain

value: wild type


title: Emb1 Rep2


title: FLe105_rep3

tag: tissue

value: forelimb


title: FLe105_run3982_rep2


title: HLe110_run3982_rep2


title: FLe105_run3982_rep1


title: Noto2 Rep3


title: Noto2 Rep1


title: Noto1 Rep3


title: HLe110Pitx1_WT_run3982_rep2

value: BALB/c


title: cml46.cml47.Pma24.Rep3

status: Public on Sep 18 2017

city: Saint Paul

first: You

last: Lu

state: MN

address: 1500 Gortner Avenue

department: Department of Plant and Microbial Biology

institute: University of Minnesota, Twin Cities

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P5_S19_R1_001

data_processing:
bcl2fastq version 2.17.1.14 was used for demultiplexing and fastq file creation.
The 5-base UMI and 3-base "GGG" were trimmed from the beginning of the read. In addition, polyA from the end of the read were also trimmed.
The trimmed reads were mapped onto the Arabidopsis TAIR10 gene model using STAR version 2.4.2a.
The STAR parameters used different from the defaults were: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0
The uniquely mapped reads were counted for each gene with no distinction among the transcript variants.
Per gene, the total read count and the UMI-based read count were weighted-averaged and rounded to an integer value, which we call the read count per gene.
Since this was 3SEQ data, no correction of the read count for the transcript length was made.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: The read count per gene for each sample was save in the .csv file. The gene names (in the AGI code) are shown as the row names, and the sample titles are shown as the column names.
Supplementary_files_format_and_content: The genes that had at least one read count across the samples are included in the processed data file.

organism: Arabidopsis thaliana

source_name: Adult leaves

growth_protocol: Thirty-day-old Arabidopsis plants grown at 22°C with 75%RH and a 12-hr light/12-hr dark cycle were used.

extract_protocol:
Total RNA was extracted from the frozen pulverized leaf tissue using TRIzol Reagent.
Smart-3SEQ, which is a modified 3SEQ method, was used (Foley et al., manuscript in preparation). The first 5 bases of the sequence read is Unique Molecular Identifier (UMI), which helps determining PCR duplicates. The following "GGG" was used for reverse transcriptase template switching. Thus, total 8 bases from the beginning of the read need to be trimmed for an actual mRNA sequence.

treatment_protocol: Two leaves per plant selected from leaf numbers 6-8 were infiltrated with either (1) Mock: 5 mM magnesium sulfate solution; or (2) Pma: suspension of Pseudomonas syringae pv. maculicola strain ES4326 in 5 mM magnesium sulfate solution at an optical density at 600 nm of 0.0002. Leaf samples were collected 24 hours after treatments.

tag: ecotype

value: cml46 cml47

value: Pma

tag: hours


title: wrky70.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P7_S32_R1_001

tag: genotype


title: Emb1 Rep1


title: cbp60a.cbp60g.sard1.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P4_S9_R1_001

value: cbp60a cbp60g sard1


title: sid2.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P8_S10_R1_001


title: wrky70.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m7_S5_R1_001

value: mock


title: chp60g.sard1.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P3_S47_R1_001

value: chp60g sard1


title: wild.type.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P1_S29_R1_001


title: cml46.cml47.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m5_S6_R1_001


title: sid2.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m8_S12_R1_001


title: Noto1 Rep1


title: chp60g.sard1.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m3_S25_R1_001


title: cbp60a.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m2_S43_R1_001


title: cbp60a.cbp60g.sard1.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m4_S20_R1_001


title: wild.type.mock24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3m1_S11_R1_001


title: wrky70.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P7_S3_R1_001


title: cbp60a.cbp60g.sard1.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P4_S38_R1_001


title: cml46.cml47.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P5_S31_R1_001


title: sid2.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P8_S7_R1_001


title: Noto1 Rep2


title: wild.type.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P1_S15_R1_001


title: sid2.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m8_S42_R1_001


title: wrky70.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m7_S39_R1_001


title: cbp60a.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P2_S44_R1_001


title: Experimental Rep6

city: St. Louis

first: Landon

middle: Kyle

last: Oetjen

state: MO

address: 660 S Euclid Avd

institute: Washington University

data_processing:
RNA-sequencing reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.  Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for each sample.

source_name: Whole Ear

extract_protocol:
Samples of murine skin were obtained and stored in RNAlater (Sigma) before processing following the manufacturer’s instructions. To extract whole tissue RNA, samples were homogenized using a bead homogenizer and processed using the Qiagen RNeasy kit following the manufacturer’s instructions. Following total RNA extraction, samples were treated with DNase (Turbo DNA-Free Kit, Thermo Scientific) following the manufacturer’s instructions before sequencing library preparation.
Library preparation was performed with 1 ug of total RNA, integrity was determined using an Agilent Bioanalyzer. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in buffer containing 40 mM Tris Acetate (pH 8.2), 100 mM Potassium Acetate, and 30mM Magnesium Acetate and heated to 94°C for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.

value: Skin

value: NaV1.8+ Jak1F/F


title: Experimental Rep5


title: cbp60a.cbp60g.sard1.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m4_S18_R1_001


title: cml46.cml47.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m5_S28_R1_001


title: Experimental Rep4


title: Experimental Rep3


title: Experimental Rep2


title: cbp60a.Pma24.Rep3

description:
project011upload_readcount_pergene.csv
processed data file column header: 3P2_S14_R1_001


title: Experimental Rep1


title: cbp60a.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m2_S33_R1_001


title: wild.type.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m1_S17_R1_001


title: Littermate Rep4

value: WT


title: sid2.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P8_S46_R1_001


title: cml46.cml47.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P5_S41_R1_001


title: Littermate Rep3


title: Littermate Rep1


title: chp60g.sard1.Pma24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2P3_S21_R1_001


title: chp60g.sard1.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P3_S8_R1_001


title: MC903 Rep4

source_name: Whole Ear_MC903


title: MC903 Rep2


title: MC903 Rep3


title: Littermate Rep2


title: sid2.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m8_S24_R1_001


title: cbp60a.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P2_S45_R1_001


title: MC903 Rep1


title: wrky70.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P7_S49_R1_001


title: PET111GFP EZ 6DO rep 1

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 sequencing machine
Adapters and low quality reads were filtered out using ea-utils software. Reads longer than 30bp with a quality score was greater than 30 were kept.
Clean reads were mapped against the TAIR 10 reference genome using the TopHat v2.0.13
Transcripts were assembled using Cufflinks (version 2.1.1). Normalized reads (FPKM values) were calculated at this step.
Genome_build: TAIR 10 reference genome
Supplementary_files_format_and_content: FPKM values for each gene in each sample. Rows are genes, columns are samples.

source_name: PET111:GFP seedlings

growth_protocol: Seeds were sterilized using 50% bleach. Seeds were imbibed in water and vernalized at 4C for 2 days. Seeds were plated on mesh squares on media containing 1xMS salts and 1% sucrose. Seeds were grown for 3,4,5,6, or 7 days.

extract_protocol:
Roots were cut and protoplasted. GFP negative cells were collected using a MoFlo cell sorter in RLT buffer and beta mercaptoethanol. RNA was extracted from sorted cells using the Qiagen RNeasy Micro Kit
cDNA synthesis and amplification was performed using the SMARTer Low Input RNA Kit for sequencing. Fragmentation was done using Covaris ultrasonicator. Libraries were prepared using the Low Input Library Prep Kit.

value: root tip

tag: developmental zone

value: elongation zone

tag: time point

value: 6 days old


title: Control Rep4

source_name: Whole Ear_control


title: wrky70.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m7_S16_R1_001organism_ch1 = Arabidopsis thaliana\n\!Sample_characteristics_ch1 = ecotype: Col-0


title: PET111GFP EZ 7DO rep 2

value: 7 days old


title: PET111GFP EZ 4DO rep 1

value: 4 days old


title: PET111GFP EZ 4DO rep 2


title: cml46.cml47.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m5_S23_R1_001


title: chp60g.sard1.mock24.Rep2

description:
project011upload_readcount_pergene.csv
processed data file column header: 2m3_S48_R1_001


title: Control Rep3


title: Control Rep1


title: PET111GFP MZ 5DO rep 2

value: meristematic zone

value: 5 days old


title: PET111GFP MZ 5DO rep 1


title: cbp60a.cbp60g.sard1.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m4_S35_R1_001


title: chp60g.sard1.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m3_S37_R1_001


title: cbp60a.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m2_S22_R1_001


title: wild.type.mock24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1m1_S36_R1_001

value: wild type


title: PET111GFP MZ 3DO rep 1

value: 3 days old


title: panW5_1

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

description: Arabidopsis QC marker_pan mutant genetic background_first biological replicate

data_processing:
cDNA libraries were sequenced using an Illumina HiSeq 2500 sequencing machine
Adapters and low quality reads were filtered out using ea-utils software. Reads longer than 30bp with a quality score was greater than 30 were kept.
Clean reads were mapped against the TAIR 10 reference genome using the TopHat v2.0.13
Transcripts were assembled using Cufflinks (version 2.1.1). Normalized reads (FPKM values) were calculated at this step.
Cuffdiff was used to test for differential expression.

source_name: Root Stem Cells

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol:
RNA was extracted using the Rneasy Micro Kit from Qiagen
cDNA synthesis and amplification was performed using the SMARTer Low Input RNA Kit for sequencing. Fragmentation was done using Covaris ultrasonicator. Libraries were prepared using the Low Input Library Prep Kit.

treatment_protocol: Seedling roots were protoplasted 5 days after germination

value: pan mutant

value: root


title: cbp60a.cbp60g.sard1.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P4_S40_R1_001

value: cbp60a cbp60g sard1

value: Pma


title: PET111GFP EZ 7DO rep 1


title: PET111GFP EZ 6DO rep 2


title: PET111GFP EZ 5DO rep 2


title: PET111GFP EZ 5DO rep 1


title: PET111GFP EZ 3DO rep 2


title: W5_1

description: Arabidopsis QC marker_WT genetic background_first biological replicate


title: wild.type.Pma24.Rep1

description:
project011upload_readcount_pergene.csv
processed data file column header: 1P1_S2_R1_001


title: Fetal_hic_r2

city: Guangzhou

last: Huang

state: Guangdong

address: Xinzao, Panyu District

department: GMU-GIBH Joint School of Life Sciences

institute: Guangzhou Medical University

description:
fetal_10k_iced.matrix.gz
fetal_40k_iced.matrix.gz

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were processed using HiC-pro
The interactions were normalized using ICE
Genome_build: hg19
Supplementary_files_format_and_content: bed files include the coordinates of genomic bins; the associated sparse matrix files include the normalized Hi-C interactions.

source_name: Fetal erythroblasts

growth_protocol: Primary fetal or adult erythroblasts were generated in vitro using a three-phase culture system.

extract_protocol: Sequencing libraries were generated using NEBNext DNA Library Prep Master Mix Set for Illumina Kit (NEB) according to the manufacturer's instructions.

value: Fetal liver

value: CD34+ derived erythroblasts

tag: differentiate stage

value: Day 11


title: Fetal_hic_r1


title: Adult_hic_r1

description:
bin_10k.bed
bin_40k.bed
adult_10k_iced.matrix.gz
adult_40k_iced.matrix.gz

source_name: Adult erythroblasts

value: Adult peripheral blood


title: PET111GFP MZ 7DO rep 2

value: root tip


title: PET111GFP EZ 3DO rep 1

value: elongation zone


title: PET111GFP MZ 7DO rep 1


title: HUDEP2_BCL11A_KO_2_BGLT3_r2

description: hudep2_BCL11A_KO_2_BGLT3_combined_nor.bedgraph

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were processed using the published pipeline (https://github.com/telenius/captureC/releases).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files include the normalized Capture-C interaction signals.

source_name: HUDEP2 cells_BCL11A_KO_2_BGLT3

growth_protocol: Primary fetal or adult erythroblasts were cultured in vitro using a three-phase culture system.

extract_protocol: Capture-C libraries were generated as described (Davies et al. 2016 Nature Methods).

tag: cell line

value: Immortalized Human Erythroid Progenitor cell line HUDEP2

value: Erythroid cells

tag: differentiation stage

value: Day 5


title: Control Rep2

value: Skin

value: WT


title: PET111GFP MZ 6DO rep 2

value: meristematic zone

value: 6 days old


title: PET111GFP MZ 6DO rep 1


title: PET111GFP MZ 4DO rep 2

value: 4 days old


title: PET111GFP MZ 3DO rep 2

value: 3 days old


title: PET111GFP MZ 4DO rep 1


title: panW5_4

description: Arabidopsis QC marker_pan mutant genetic background_forth biological replicate

value: pan mutant

value: root


title: HUDEP2_delHBBP1_1_BGLT3_r2

description: hudep2_delHBBP1_1_BGLT3_combined_nor.bedgraph

source_name: HUDEP2 cells_delHBBP1_1_BGLT3


title: panW5_3

description: Arabidopsis QC marker_pan mutant genetic background_third biological replicate


title: panW5_2

description: Arabidopsis QC marker_pan mutant genetic background_second biological replicate


title: HUDEP2_delHBBP1_1_HS3_r2

description: hudep2_delHBBP1_1_HS3_combined_nor.bedgraph

source_name: HUDEP2 cells_delHBBP1_1_HS3


title: W5_4

description: Arabidopsis QC marker_WT genetic background_forth biological replicate

value: wild type


title: HUDEP2_HS3_r2

source_name: HUDEP2 cells_HS3


title: HUDEP2_HS3_r1


title: W5_3

description: Arabidopsis QC marker_WT genetic background_third biological replicate


title: W5_2

description: Arabidopsis QC marker_WT genetic background_second biological replicate


title: Adult_hic_r2

value: CD34+ derived erythroblasts


title: HUDEP2_BCL11A_KO_2_BGLT3_r1


title: A_bglobins_r1

description:
a_HBB_combined_nor.bedgraph
a_HBG2_combined_nor.bedgraph

source_name: A_bglobins_Adult erythroblasts

value: Day 11


title: A_bglobins_r2

value: Adult peripheral blood


title: HUDEP2_BCL11A_KO_2_HS3_r2

description: hudep2_BCL11A_KO_2_HS3_combined_nor.bedgraph

source_name: HUDEP2 cells_BCL11A_KO_2_HS3


title: HUDEP2_BCL11A_KO_2_HS3_r1


title: HUDEP2_BCL11A_KO_1_BGLT3_r2

description: hudep2_BCL11A_KO_1_BGLT3_combined_nor.bedgraph

source_name: HUDEP2 cells_BCL11A_KO_1_BGLT3


title: HUDEP2_BCL11A_KO_1_HS3_r2

description: hudep2_BCL11A_KO_1_HS3_combined_nor.bedgraph

source_name: HUDEP2 cells_BCL11A_KO_1_HS3


title: HUDEP2_BCL11A_KO_1_HS3_r1


title: A_HBBP1_r1

source_name: A_HBBP1_Adult erythroblasts


title: F_HBBP1_r1

source_name: F_HBBP1_Fetal erythroblasts

value: Fetal liver


title: HUDEP2_delHBBP1_2_BGLT3_r2

description: hudep2_delHBBP1_2_BGLT3_combined_nor.bedgraph

source_name: HUDEP2 cells_delHBBP1_2_BGLT3


title: HUDEP2_delHBBP1_2_BGLT3_r1


title: HUDEP2_delHBBP1_1_BGLT3_r1


title: HUDEP2_delHBBP1_2_HS3_r2

description: hudep2_delHBBP1_2_HS3_combined_nor.bedgraph

source_name: HUDEP2 cells_delHBBP1_2_HS3


title: HUDEP2_delHBBP1_1_HS3_r1


title: HUDEP2_delHBBP1_2_HS3_r1


title: HUDEP2_BGLT3_r2

source_name: HUDEP2 cells_BGLT3


title: F_3HS1_r2

source_name: F_3HS1_Fetal erythroblasts


title: HUDEP2_BGLT3_r1


title: H9_HBBP1_r1

source_name: H9_HBBP1_Embryonic stem cells

value: Embryonic stem cells


title: F_HS5_r2

source_name: F_HS5_Fetal erythroblasts


title: H9_bglobins_r2

description:
h9_HBB_combined_nor.bedgraph
h9_HBG2_combined_nor.bedgraph

source_name: H9_bglobins_Embryonic stem cells


title: HUDEP2_BCL11A_KO_1_BGLT3_r1

value: Immortalized Human Erythroid Progenitor cell line HUDEP2


title: H9_bglobins_r1


title: F_bglobins_r2

description:
f_HBB_combined_nor.bedgraph
f_HBG2_combined_nor.bedgraph

source_name: F_bglobins_Fetal erythroblasts


title: F_HBBP1_r2


title: A_HBBP1_r2


title: H9_3HS1_r1

source_name: H9_3HS1_Embryonic stem cells


title: H9_3HS1_r2


title: F_3HS1_r1


title: A_3HS1_r1

source_name: A_3HS1_Adult erythroblasts


title: H9_HS5_r2

source_name: H9_HS5_Embryonic stem cells


title: Fetal_CTCF_ChIPSeq_r1

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome hg19 with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with read coverage

source_name: Fetal erythroblasts_CTCF_ChIP

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Libraries were prepared using TruSeq ChIP-seq Sample Preparation Kit (Part# IP-202-1012) according to Illumina's instructions.

value: Day 14

tag: chip antibody


title: RNA-seq_fetal_d14_r1

data_processing:
Basecalls using bcl2fastq2 v2.15.0.4, and parameters --no-eamss --mismatches 1
Reads were aligned using STAR.
The FPKM were normalized to ERCC spike-in control.
Genome_build: hg19
Supplementary_files_format_and_content: Text file includes normalized FPKM.

source_name: fetal erythroblasts_d14

extract_protocol:
Total RNA was extracted using TRIzol according to manufacturer's instructions
RNA-seq libraries were constructed using the ScriptSeq Complete kit (Illumina) according to manufacturer’s instructions.


title: H9_HS5_r1


title: F_bglobins_r1


title: F_HS5_r1


title: H9_HS3_r2

source_name: H9_HS3_Embryonic stem cells


title: H9_HS3_r1


title: A_HS3_r2

source_name: A_HS3_Adult erythroblasts


title: RNA-seq_adult_d11_r1

source_name: adult erythroblasts_d11


title: H9_HBBP1_r2


title: A_HS3_r1


title: F_HS3_r2

source_name: F_HS3_Fetal erythroblasts


title: F_HS3_r1


title: A_3HS1_r2


title: RNA-seq_fetal_d14_r2


title: Adult_CTCF_input

description: input DNA

source_name: Adult erythroblasts_CTCF_input


title: Adult_CTCF_ChIPSeq_r2

source_name: Adult erythroblasts_CTCF_ChIP


title: RNA-seq_fetal_d11_r1

source_name: fetal erythroblasts_d11


title: Fetal_CTCF_ChIPSeq_r2


title: A_HS5_r2

source_name: A_HS5_Adult erythroblasts


title: RNA-seq_adult_d14_r1

source_name: adult erythroblasts_d14


title: RNA-seq_fetal_d11_r2


title: RNA-seq_adult_d14_r2


title: A_HS5_r1


title: T55E

city: Witten

first: Claudia

last: Hagedorn

address: Stockumer Strasse 10

department: Chair for Biochemistry and Molecular Medicine

country: Germany

institute: Witten/ Herdecke University

description:
HeLa_pEPI
Processed data file: CuffDiff wt-vs-pEPI_Galaxy_gene.txt
Processed data file: CuffDiff wt-vs-pEPI_Galaxy_transcripts.txt

data_processing:
Illumina 1.9 was used for conventional base calling.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 withTophat2 for Illumina (Galaxy Version 2.0.9) applying default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al. (Kim, D et al., Genome Biol 2013, 14, R36; Trapnell et al., Nature protocols 2012, 7, 562; Trapnell et al., Nat Biotechnol 2010, 28, 511).
Significant changes in transcript expression were calculated with CuffDiff (Galaxy Version 2.2.1.3) setting false discovery rate to 0.01.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values for each sample (Cufflinks) and results of differential expression testing for transcripts and genes (CuffDiff; FPKM of WT vs. FPKM of T55E).
Supplementary_files_format_and_content: bigWig: BigWig files contain mapped reads for visualisation in the UCSC Genome Browser as a graph.

source_name: HeLa, pEPI-EGFP transfected

extract_protocol:
RNA was extracted using Trizol reagent. NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) was used to purify mRNA from 1μg total RNA. NEBNext® mRNA Library Prep Reagent Set for Illumina (NEB #E6100) was used with 250ng mRNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HeLa cells were transfected with 2μg plasmid DNA (S/MAR-based episome pEPI-EGFP). Transfected cells were selected 48h post-transfection for 14d. Established S/MAR-based episomes are then maintained stably in the absence of selection.

value: HeLa

tag: tissue origin

value: cervix carcinoma

tag: transfection

value: pEPI-EGFP


title: WT

description:
HeLa_wt
Processed data file: CuffDiff wt-vs-pEPI_Galaxy_gene.txt
Processed data file: CuffDiff wt-vs-pEPI_Galaxy_transcripts.txt

source_name: HeLa


title: Adult_CTCF_ChIPSeq_r1


title: primary_T_DMSO_2

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
RNA-seq after 6hr DMSO (0.1%) treatment
processed data file: primary_T_all_fpkm_exprs_norm.txt

data_processing:
alignment: HiSat using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. FPKM values were ERCC normalized. See methods for further details
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript

source_name: primary T cell

growth_protocol: Alpha-MEM with Glutamax-1, 10% FBS, 10% human AB serum, 1% L-glutamine, 1% penicillin/streptomycin, 1X Insulin-Transferrin-Selenium, 10 ng/mL recombinant mouse IL-7, and 10 ng/mL recombinant IL-2

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
RNA libraries were prepared for sequencing using SMARTer v4 Low Input RNA Kit from Clontech

value: primary T cell

tag: bar code

value: TCGAAGTG


title: primary_T_DMSO_1

value: TTCCATTG


title: primary_T_dBET6_2

description:
RNA-seq after 6 hr dBET6 (250 nM) treatment
processed data file: primary_T_all_fpkm_exprs_norm.txt

value: TTGGTATG


title: primary_T_JQ1_1

description:
RNA-seq after 6hr JQ1 (1 µM) treatment
processed data file: primary_T_all_fpkm_exprs_norm.txt

value: GGCACAAC


title: MOLT4_Pol2_input

description: input sample for background measurement

data_processing:
For all samples, reads were aligned to their indicated build using bowtie2 with parameters -k 1.
MACS1.4 with p-value = 1e-9 and default parameters was used to call peaks and generate wiggles.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples, aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL

growth_protocol: Cells were cultured in RPMI-10%FCS.

extract_protocol:
Standard DNA extraction from MOLT4 cell lines using cell lysis. Probe sonicator 3 minutes total sonication time (1 sec on, 4 sec off, 60% amplitude) on ice.
Library prep with Rubicon TruePlex kit.

tag: antibody

tag: antibody manufacturer

tag: antibody catalog number

tag: drug treatment

tag: input sample

tag: sequencing barcode

value: TCTGCTGT


title: MOLT4_Pol2_JQ1

description: Chromatin IP against RNA Pol II

value: RNA Pol II

value: Diagenode

value: JQ1 (1 uM) for 2 hours

value: TGCGATCT


title: primary_T_dBET6_3

tag: cell type

value: TGAACTGG


title: MOLT4_Pol2_DMSO

description: Chromatin IP against RNA Pol II

value: DMSO for 2 hours

value: GGTTGGAC


title: PDX_TALL_dBET6_1

description:
RNA-seq after 6 hr dBET6 (250 nM) treatment
processed data file: PDX_TALL_all_fpkm_exprs_norm.txt

source_name: T-ALL PDX

value: T-ALL PDX

value: TCATTGAG


title: PDX_TALL_JQ1_2

description:
RNA-seq after 6hr JQ1 (1 µM) treatment
processed data file: PDX_TALL_all_fpkm_exprs_norm.txt

value: TACTAGTC


title: PDX_TALL_JQ1_1

value: TCAGATTC


title: PDX_TALL_DMSO_3

description:
RNA-seq after 6hr DMSO (0.1%) treatment
processed data file: PDX_TALL_all_fpkm_exprs_norm.txt

value: TGTATGCG


title: primary_T_JQ1_3

value: primary T cell

value: TCAGGAGG


title: primary_T_JQ1_2

value: TCTCACGG


title: PDX_TALL_dBET6_3

value: TATGCCAG


title: RNA-seq_adult_d11_r2

tag: tissue

value: Adult peripheral blood

value: CD34+ derived erythroblasts

value: Day 11


title: PDX_TALL_DMSO_2

value: TCCAGTCG


title: PDX_TALL_dBET6_2

value: TGGCTCAG


title: PDX_TALL_JQ1_3

value: TTCAGCTC


title: MOLT4_H3K27ac_INPUT

growth_protocol: cells were cultured in RPMI-10%FCS

extract_protocol:
Standard DNA extraction from MOLT4 cell lines using cell lysis.
Probe sonicator 3 minutes total sonication time (1 sec on, 4 sec off, 60% amplitude) on ice library prep with Rubicon TruePlex kit.


title: MOLT4_BRD4_dBET6

value: Bethyl


title: MOLT4_JQ1_pS2_POL2

value: RNA pol II CTD phospho Ser2

value: Active Motif


title: PDX_TALL_DMSO_1

value: T-ALL PDX

value: TAAGTTCG


title: Fetal_CTCF_input

description: input DNA

source_name: Fetal erythroblasts_CTCF_input

value: Fetal liver


title: primary_T_dBET6_1

value: TAACGCTG


title: MOLT4_BRD4_JQ1


title: MOLT4_H3K27ac

value: Abcam


title: MOLT4_BRD4_INPUT


title: MOLT4_BRD4_DMSO

value: DMSO


title: MOLT4_Pol2_dBET6

description: Chromatin IP against RNA Pol II

value: RNA Pol II

value: Diagenode

value: dBET6 (100 nM) for 2 hours

value: TTCCTGCT


title: MOLT4_CDK9_INPUT


title: MOLT4_CDK9_DMSO

value: Santa Cruz


title: MOLT4_dBET6_pS2_POL2


title: NET-seq dBET6 Rep2

data_processing:
Reads are trimmed and aligned using STAR (v2.4.0) (Dobin et al., 2013)
For NET-seq data, only the position matching the 50 end of the sequencing read (after removal of the barcode), corresponding to the 30 end of the nascent RNA fragment, is recorded with a Python script using HTSeq package (Anders et al., 2015). Reverse transcription mispriming events are identified and removed when molecular barcode sequences match exactly to the genomic sequence adjacent to the aligned read. Reads that align to the same genomic position and contain identical barcodes are considered PCR duplication events and are removed. Splicing intermediates have 30 hydroxyls and will enter NET-seq libraries and contribute to the reads aligning to the exact single-nucleotide 30 ends of introns and 30 ends of exons.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: BedGraph files (http://genome.ucsc.edu/goldenPath/help/bedgraph.html); Column1=chromosome; Column2=start (left most coordinate; 0 based; position included); Column3=end (right most coordinate; 0 based; position not included); Column4=Coverage (3'end nt for NET-seq and whole read for RNA-seq)

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
For NET-seq, the library preparation is performed as described by Churchman and Weissman (2011, 2012) with modifications. For 30 RNA ligation, a pre-adenylated DNA linker with a mixed random hexameric barcode sequence at its 50 end is used. cDNA containing the 30 end sequences of a subset of mature and heavily sequenced snRNAs, snoRNAs, rRNAs, and mitochondrial tRNAs are specifically depleted using biotinylated DNA oligos, as described by Ingolia et al.

tag: library type

value: 3'end RNA fragment sequencing

tag: treatment

tag: molecule subtype

value: nascent RNA


title: NET-seq JQ1 Rep1

tag: cell line


title: NET-seq JQ1 Rep2


title: NET-seq DMSO Rep2

source_name: DMSO


title: MOLT4_CDK9_dBET6


title: NET-seq dBET6 Rep1


title: MOLT4_CDK9_JQ1