title: hsp1-2

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: genomic DNA from two-timepoint editing, control, no heat shock

data_processing:
Single-cell RNA Sequencing data (FASTQ files) were processed using the inDrops.py bioinformatics pipeline available at https://github.com/indrops/indrops.
Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 (release-86) genome assembly.
Bowtie version1.1.1 was used with parameter –e 200; UMI quantification was used with parameter –u 2 (counts were ignored from UMIs split between more than 2 genes).
genomic DNA GESTALT and scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping
Genome_build: GRCz10
CSV files for transcriptome data were generated using the inDrops pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for genes. Txt files for genomic DNA GESTALT libraries (*allReadCounts) contain lineage barcode sequences (HMID column) for each cell and their proportion in the sequenced libraries. scGESTALT data (*GestMaster.txt) contains the inDrops cell identifiers (CellBarcode and BarcodeKey) that were used to match barcodes to transcriptomes. They also contain lineage barcode sequences (HMID column) for each cell with a corresponding inDrops single-cell gene expression profile, as well as the the t-SNE cluster membership number (ClusterIdent column)
Txt files ending in *stats.txt contain information about the each individually captured UMI or cell per sample. The barcode sequence aligned to a reference unedited sequence (mergedRead column), mutations at each target site (target[X] columns) and the edited sequences at each target site (sequence[X] columns) were used for downstream analysis.
inDropsExpMatrix_noQ txt file is the gene expression matrix for the full dataset. Columns are individual cells from different batches of whole brains (f1_, f2_, f3_, f4_, f5_, f6_) or brain regions (fore_, mid_, hind_). fall.inDrops.Robj is the processed Seurat R object, which can be loaded into R and explored.

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Genomic DNA was extracted using DNeasy kit (Qiagen)
Samples were UMI tagged and PCR amplified using primers flanking the barcode as described in McKenna et al., Science, 2016. Sequencing adapters, sample indexes and flow cell adapters were incorporated by PCR, and libraries were quantified using the NEBNext Library Quant kit (NEB).

value: whole embryo

tag: developmental stage

value: 55 hpf


title: hsp1-1

status: Public on Feb 09 2018

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: tissue


title: icell8 382

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
Neg_26
H2O was used as input

library_source: transcriptomic

data_processing:
Sequence reads in Fastq format were generated from Illunina basecalls using Illumina's bcl2fastq (version 2.17).
Sequence reads were aligned to Ensembl GRCh37 genome build and gene models retrieved from Illumina's igenome using Tophat2 (v 2.0.11).
Aligned reads were counted whithin exons using Rsubread (verion 1.22.3)
Genome_build: h19
Supplementary_files_format_and_content: counts of genes

molecule: total RNA

organism: Homo sapiens

source_name: no cell

growth_protocol: IMR90 fibroblasts were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
RNA-Seq libraries were prepared following the iCELL8 Single-Cell protocol (WaferGen Biosystems).
Nextera XT Library Preparation (Illumina) adapted for iCELL8 Single-Cell libraries (WaferGen Biosystems)

treatment_protocol: Cells were transduced with retroviral OSKM expression or control vectors followed by lentiviral shRNA vectors and selected with G418 and puromycin, respectively. At 16 days post-infection, cells were dispensed on the iCELL8 microchip.

tag: cell line

value: no cell

tag: transduction

value: no vector


title: icell8 378

source_name: IMR90 fibroblast

value: IMR90 fibroblast

value: OSKM + shRNA library


title: icell8 383


title: icell8 376


title: icell8 375


title: icell8 379

description:
Pos_26
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector

value: control vector


title: icell8 377


title: icell8 384


title: icell8 380


title: icell8 385


title: icell8 373

description:
Neg_25
H2O was used as input


title: icell8 401


title: hsp2-8

description: genomic DNA from two-timepoint editing, control, only heat shock


title: hsp5-3

description: genomic DNA from two-timepoint editing, injection + heat shock


title: hsp5-7


title: hsp5-8


title: hsp5-6


title: icell8 374


title: icell8 371

description:
Pos_25
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: hsp5-5


title: icell8 372


title: icell8 370


title: icell8 369


title: icell8 381


title: hsp5-2


title: hsp5-4


title: hsp5-1


title: hsp2-7


title: icell8 368


title: icell8 364

description:
Neg_27
H2O was used as input


title: icell8 367


title: icell8 360


title: icell8 366


title: icell8 365


title: DEW154_hind

description:
inDrops Transcriptome libraries DEW152-DEW154, Hind
GSTLT_hind.noQ.genes.csv.gz

source_name: zebrafish brain

extract_protocol:
Single-cell suspensions were processed through inDrops to generate single-cell cDNA libraries. cDNAs were in vitro transcribed and fragmented. The 3' fragments were reverse transcribed and prepared for sequencing
Libraries were prepared as described in Zilionis et al., 2017, Nature Protocols (PMID = 27929523)

value: brain


title: icell8 363


title: DEW157_mid

description:
inDrops Transcriptome libraries DEW155-DEW157, Mid
GSTLT_mid.noQ.genes.csv.gz


title: DEW155_mid


title: icell8 359


title: icell8 361


title: DEW152_hind


title: DEW153_hind


title: icell8 355


title: icell8 356


title: DEW146_f6

description:
inDrops Transcriptome libraries DEW142-DEW148, Fish6
GSTLT_f6.noQ.genes.csv.gz


title: DEW150_fore

description:
inDrops Transcriptome libraries DEW149-DEW151, Fore
GSTLT_fore.noQ.genes.csv.gz


title: icell8 358


title: DEW145_f6


title: icell8 352


title: icell8 357


title: DEW149_fore


title: DEW144_f6


title: DEW147_f6


title: icell8 354


title: DEW148_f6


title: DEW143_f6


title: icell8 353

description:
Neg_18
H2O was used as input


title: DEW156_mid


title: icell8 350

description:
Neg_21
H2O was used as input


title: icell8 351

description:
Pos_21
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: DEW142_f6


title: icell8 349


title: DEW151_fore


title: icell8 362


title: DEW141_f5

description:
inDrops Transcriptome libraries DEW135-DEW141, Fish5
GSTLT_f5.noQ.genes.csv.gz


title: DEW140_f5


title: icell8 348


title: icell8 347


title: DEW137_f5


title: DEW139_f5


title: icell8 346

description:
Pos_23
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: DEW136_f5


title: DEW135_f5


title: DEW138_f5


title: icell8 344


title: DEW134_f4

description:
inDrops Transcriptome libraries DEW123-DEW134, Fish4
GSTLT_f4.noQ.genes.csv.gz


title: icell8 341


title: icell8 345


title: DEW133_f4


title: icell8 343


title: icell8 338


title: icell8 340


title: icell8 339


title: DEW129_f4


title: icell8 336


title: DEW128_f4


title: DEW131_f4


title: icell8 337


title: icell8 334


title: DEW130_f4


title: icell8 333


title: DEW125_f4


title: icell8 335


title: DEW126_f4


title: DEW124_f4


title: DEW127_f4


title: icell8 342


title: icell8 332


title: DEW123_f4


title: DEW132_f4


title: icell8 330


title: icell8 329


title: icell8 328

description:
Neg_19
H2O was used as input


title: icell8 327


title: DEW119_f3

description:
inDrops Transcriptome libraries DEW111-DEW122, Fish3
GSTLT_f3.noQ.genes.csv.gz


title: DEW120_f3


title: icell8 326


title: DEW118_f3


title: icell8 323


title: DEW116_f3


title: icell8 324


title: DEW117_f3


title: icell8 322


title: DEW115_f3


title: DEW114_f3


title: DEW113_f3


title: icell8 319

description:
Neg_20
H2O was used as input


title: DEW111_f3


title: icell8 320


title: DEW122_f3


title: DEW112_f3


title: DEW121_f3


title: icell8 317


title: DEW067_f2

description:
inDrops Transcriptome libraries DEW064-DEW067, Fish2
GSTLT_f2.noQ.genes.csv.gz


title: icell8 331


title: DEW066_f2


title: DEW065_f2


title: icell8 318


title: icell8 315


title: icell8 316

description:
Pos_22
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: DEW064_f2


title: icell8 313

source_name: K562 myeloid leukemia

value: K562 myeloid leukemia


title: DEW063_f1

description:
inDrops Transcriptome libraries DEW058-DEW063, Fish1
GSTLT_f1.noQ.genes.csv.gz


title: DEW062_f1


title: icell8 314


title: icell8 312


title: icell8 321


title: icell8 325


title: DEW061_f1


title: icell8 311


title: icell8 310


title: DEW059_f1


title: DEW058_f1


title: icell8 308


title: icell8 309


title: icell8 297


title: icell8 299


title: icell8 303


title: icell8 298


title: icell8 301


title: icell8 302


title: icell8 296


title: icell8 300


title: icell8 304


title: icell8 288


title: icell8 291


title: icell8 292


title: icell8 289


title: icell8 294


title: icell8 295


title: icell8 293


title: DEW060_f1


title: icell8 287


title: icell8 286


title: icell8 284


title: icell8 282


title: icell8 283


title: icell8 281


title: icell8 279


title: icell8 280


title: icell8 305


title: icell8 307


title: icell8 306


title: icell8 290


title: icell8 277


title: icell8 276


title: icell8 273

description:
Pos_19
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 274


title: icell8 272


title: icell8 271


title: icell8 270


title: icell8 285

description:
Pos_17
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 261


title: icell8 264


title: icell8 268

description:
Neg_17
H2O was used as input


title: icell8 265


title: icell8 260


title: icell8 266


title: icell8 262

description:
Pos_18
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 269


title: icell8 263


title: icell8 257


title: icell8 267


title: ZT10 αKO Hi-C rep1

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Hi-C libraries have been aligned to mm9 and processed using Hi-C Pro verision 2.7.7
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0.
Tag directories were called using homer
Genome_build: mm9
Supplementary_files_format_and_content: Matrix files are tab-delimited files which includes three columns: bini,binj, and the ICE-normalized interaction between bini and binj.
Tag directory files include the tag count at each base pair position.
Bed file (mm9_5000_ord.bed.gz) include the  mappping of each bin in terms of the genome position, based on mm9.

organism: Mus musculus

source_name: ZT10 αKO Hi-C

growth_protocol: Male wild-type and Rev-erb alpha KO mice maintained on a C57BL/6 background maintained on a 12 hour dark/light cycle.

extract_protocol:
Genomic DNA was isolated by phenol:chloroform extraction followed by cloroform wash.
Nuclei isolation: Mouse liver tissue (100mg) was dounced with 15 mL of cold swelling buffer (10mM HEPES, 2mM MgCl2, 3mM CaCl3) 10 times with piston A. After 20 min incubation on ice, the homogenate was dounced again 20 times with piston B, after which additional 15mL of cold swelling buffer was added. The homogenate was filtered through a 100mm cell strainer and spun at 400g in 4°C for 10 min. The supernatant was discarded, and the pellet resuspended in 10mL of cold swelling buffer containing 10% glycerol. 10mL of cold lysis buffer (swelling buffer + 10% glycerol +1% Igepal) was slowly added with occasional vortexing. After 5 min incubation on ice, 30mL of cold lysis buffer was added, after which it was spun down at 600g in 4°C for 5 min. The supernatant was discarded and the pellet resuspended with 25mL of cold lysis buffer and spun down at 600g at 4°C for 5 min again. The supernatant was discarded, and the pellet contained isolated, undisrupted nuclei. For ChIP and Hi-C experiments, these pure nuclei were crosslinked in 10 mL of PBS with 1% formaldehyde for 20 min at room temperature and quenched with 1/20 volume of 2.5M glycine solution for 5 min. The crosslinked nuclei were spun down at 600g at 4°C for 5 min, after which they were resuspended in Hi-C lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% Igepal) and spun down at 600g in 4°C for 5 min again. The supernatant was discarded, and crosslinked nuclei was used for ChIP and Hi-C.
ChIP-seq: 1-5 million crosslinked nuclei were used per immunoprecipitation. Nuclear extract were prepared by sonication in lysis buffer (50mM Tris-HCl pH 8, 0.1% SDS, 10mM EDTA) using the Bioruptor (Diagenode) for a fragment range of 200-1000bp. Chromatin was immunoprecipitated in ChIP buffer (50mM Tris-HCl pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% NaDOC) using 5-10ug of antibody, and reverse crosslinked overnight at 65°C in SDS buffer (50mM Tris-HCl, 10mM EDTA, 1% SDS, pH 8). DNA was isolated using phenol/chloroform/isoamyl alcohol and second chloroform wash.
Hi-C: In situ Hi-C was performed with mouse liver tissues using MboI restriction enzyme based on the protocol provided by Rao et al. Cell 2014 (PMID: 25497547) with minor changes described below. In addition, biotin from unligated ends were removed by incubating 5ug of DNA in 50ul T4 DNA polymerase reaction (0.1ug/ul BSA, 1xNEB buffer 2, 25uM dGTP, 15U T4 DNA polymerase). The reaction was carried out at room temperature for 4 hours and stopped by the addition of 2ul of 0.5M EDTA pH 8.0 per 50ul reaction. Isolated Hi-C DNA was amplified by fewer than 8 PCR cycles to reduce PCR duplicates.

treatment_protocol: 8-12 weeks old mice are sacrificed at ZT22 (5AM) or ZT10 (5PM)

value: Liver

tag: background strain

tag: genotype

value: NR1D1 knockout

tag: time


title: icell8 258


title: icell8 259


title: icell8 256


title: ZT10 αKO Hi-C rep2


title: icell8 255


title: icell8 278


title: icell8 254


title: ZT10 αKO Hi-C rep3


title: icell8 253


title: icell8 252


title: icell8 275


title: icell8 251


title: ZT10 Hi-C rep2

source_name: ZT10 Hi-C

value: Wild type


title: ZT10 Hi-C rep1


title: ZT22 Hi-C rep5

source_name: ZT22 Hi-C


title: ZT22 Hi-C rep4


title: ZT22 Hi-C rep3


title: icell8 247


title: ZT22 Hi-C rep1


title: icell8 245


title: icell8 246


title: icell8 250

description:
Pos_16
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 249

description:
Pos_20
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 242


title: icell8 241


title: icell8 244


title: icell8 240


title: icell8 235


title: icell8 236


title: icell8 234


title: icell8 243


title: icell8 233


title: icell8 237


title: icell8 231


title: icell8 228


title: icell8 239


title: icell8 226


title: icell8 225


title: icell8 227


title: icell8 224

description:
Neg_15
H2O was used as input


title: icell8 229


title: ZT22 Hi-C rep2


title: icell8 248


title: icell8 238


title: icell8 223

description:
Pos_11
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 232


title: icell8 221


title: icell8 218


title: icell8 216

description:
Neg_16
H2O was used as input


title: icell8 219


title: icell8 220


title: icell8 230


title: icell8 222

description:
Pos_14
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 213


title: icell8 212


title: icell8 217


title: icell8 214


title: icell8 206


title: icell8 209

description:
Pos_12
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 205


title: icell8 215


title: icell8 210


title: icell8 211


title: icell8 203


title: icell8 208


title: icell8 200


title: icell8 201

description:
Pos_13
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 207

description:
Pos_15
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 204


title: icell8 198


title: icell8 199


title: icell8 202


title: icell8 197


title: icell8 196


title: icell8 195


title: icell8 193


title: icell8 194


title: icell8 191


title: icell8 189


title: icell8 187


title: icell8 188


title: icell8 179


title: icell8 186


title: icell8 184


title: icell8 192


title: icell8 182


title: icell8 183


title: icell8 178


title: icell8 181

description:
Neg_10
H2O was used as input


title: icell8 177

description:
Neg_13
H2O was used as input


title: icell8 168


title: icell8 174


title: icell8 171


title: icell8 175


title: icell8 176

description:
Pos_10
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 173


title: icell8 167


title: icell8 166

description:
Neg_12
H2O was used as input


title: icell8 170


title: icell8 190


title: icell8 172


title: icell8 165


title: icell8 185


title: icell8 164


title: icell8 161


title: icell8 160

description:
Neg_11
H2O was used as input


title: icell8 169


title: icell8 180


title: icell8 159


title: icell8 156


title: icell8 163


title: icell8 162


title: icell8 158

description:
Neg_14
H2O was used as input


title: icell8 154


title: icell8 152


title: icell8 155


title: icell8 150


title: icell8 151


title: icell8 148


title: icell8 147


title: icell8 144


title: icell8 142


title: icell8 149


title: icell8 139


title: icell8 145


title: icell8 141


title: icell8 138


title: icell8 153


title: icell8 140


title: icell8 135


title: icell8 137


title: icell8 136


title: icell8 132


title: icell8 130


title: icell8 131


title: icell8 134


title: icell8 133


title: icell8 129


title: icell8 126


title: icell8 124


title: icell8 123


title: icell8 125


title: icell8 121


title: icell8 120

description:
Neg_06
H2O was used as input


title: icell8 119


title: icell8 116


title: icell8 118

description:
Pos_05
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 117

description:
Neg_08
H2O was used as input


title: icell8 115


title: icell8 113


title: icell8 128


title: icell8 112


title: icell8 114

description:
Pos_09
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 109


title: icell8 111


title: icell8 127


title: icell8 108

description:
Pos_07
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 105


title: icell8 107


title: icell8 103


title: icell8 106


title: icell8 101


title: icell8 104


title: icell8 122


title: icell8 102


title: icell8 100


title: icell8 97


title: icell8 98


title: icell8 93


title: icell8 99

description:
Neg_07
H2O was used as input


title: icell8 91


title: icell8 90


title: icell8 88


title: icell8 157


title: icell8 89


title: icell8 143


title: icell8 83


title: icell8 85


title: icell8 95

description:
Neg_09
H2O was used as input


title: icell8 87


title: icell8 86


title: icell8 84

description:
Pos_08
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 77


title: icell8 79


title: icell8 78


title: icell8 82


title: icell8 76


title: icell8 81


title: icell8 75


title: icell8 96

description:
Pos_06
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 94


title: icell8 92


title: icell8 73


title: icell8 72


title: icell8 71


title: icell8 70


title: icell8 69


title: icell8 65


title: icell8 110


title: icell8 67


title: icell8 64


title: icell8 61


title: icell8 62


title: icell8 63


title: icell8 66


title: icell8 59


title: icell8 53


title: icell8 58


title: icell8 56


title: icell8 51


title: icell8 50


title: icell8 54


title: icell8 48


title: icell8 55


title: icell8 49


title: Rev-erbα ZT10 αKO rep2

source_name: Rev-erbα ZT10 αKO

tag: chip antibody

value: Cell Signaling (2124)


title: Rev-erbα ZT10 αKO rep1


title: icell8 45


title: icell8 52


title: Rev-erbα ZT10 rep1

source_name: Rev-erbα ZT10


title: icell8 46


title: icell8 74


title: BRD4 ZT22

source_name: BRD4 ZT22


title: Rev-erbα ZT22 rep2

source_name: Rev-erbα ZT22


title: icell8 43


title: RAD21 ZT10 rep2

source_name: RAD21 ZT10

value: Abcam (ab992)


title: BRD4 ZT10 αKO

source_name: BRD4 ZT10 αKO


title: RAD21 ZT10 rep1


title: RAD21 ZT22 rep2

source_name: RAD21 ZT22


title: icell8 57


title: icell8 42


title: icell8 41


title: RAD21 ZT22 rep1


title: MED1 ZT10 αKO

source_name: MED1 ZT10 αKO


title: Rev-erbα ZT10 rep2


title: MED1 ZT10

source_name: MED1 ZT10


title: MED1 ZT22

source_name: MED1 ZT22


title: icell8 47


title: icell8 39


title: BRD4 ZT10

source_name: BRD4 ZT10


title: icell8 38

source_name: IMR90 fibroblast


title: CTCF ZT22

source_name: CTCF ZT22

value: Millipore (07-729)


title: CTCF ZT10

source_name: CTCF ZT10


title: icell8 37

source_name: K562 myeloid leukemia


title: icell8 35


title: icell8 32


title: icell8 31


title: icell8 33


title: icell8 30


title: icell8 29


title: icell8 68


title: icell8 24

description:
Neg_05
H2O was used as input

source_name: no cell


title: icell8 40


title: icell8 34

description:
Pos_02
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 146


title: icell8 20


title: icell8 19


title: icell8 27


title: icell8 26

description:
Neg_01
H2O was used as input


title: icell8 18


title: icell8 25


title: icell8 80


title: icell8 23


title: icell8 15

description:
Neg_04
H2O was used as input


title: icell8 60


title: icell8 22


title: icell8 11


title: icell8 10


title: icell8 8


title: icell8 21

description:
Pos_04
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 36

description:
Neg_03
H2O was used as input


title: icell8 16


title: icell8 13


title: icell8 12

description:
Pos_03
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 2


title: Prolactin HC11  Rep 2 (PRL)

city: Hyderabad

first: Sreenivasulu

last: Kurukuti

state: Telangana

address: Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

data_processing:
FastqQC to check quality of the data and to remove  adapters from sequencing reads, it also removes reads containing N > 10% (N represents the base cannot be determined)and  reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Paired end senquencing reads were mapped to the reference genome by using TopHat2 tool. Mismatch parameter was kept as 2 and remaining all parameters were set as default.
Gene expression level is measured by transcript abundance. The greater the abundance, the higher is the gene expression level. In our RNA-seq analysis, the gene expression level is estimated by counting the reads that map to genes or exons. Read count is not only proportional to the actual gene expression level, but is also proportional to the gene length and the sequencing depth. In order for the gene expression levels estimated from different genes and experiments to be comparable, the FPKM is used. In RNA-seq, FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs-sequenced, is the most common method of estimating gene expression levels, which takes into account the effects of both sequencing depth and gene length on-counting of fragments (Trapnell, Cole, et al., 2010).
The correlation between samples is an important indicator for testing the reliability of the experiment. The closer the correlation coefficient is to 1, the greater the similarity of the samples. ENCODE suggests that the square of the Pearson correlation coefficient should be larger than 0.92, under ideal experimental conditions
After gene expression abundance we performed differential gene expression by using DESeq2 (Anders et al, 2016). The differential gene expression analysis contains three steps: 1) Read counts Normalization; 2) Model dependent p-value estimation; negative binomial distribution 3)FDR value estimation based on multiple hypothesis testing.
Genome_build: UCSC mm10 mouse genome assembly

source_name: Mouse HC11 cell line

growth_protocol: Embryonic stem cells (R1 Cells) were grown on feeder cells with Lif, serum and 2i inhibitors till 50-60% confluency.  HC11 normal cells were grown in RPMI1640-GlutaMAXTM complete medium with stage specific treatment as given below.

extract_protocol:
Total RNA was extracted from ESC, Normal, Primed and Prolactin samples in replicates by using TRIzol reagent according to manufacturer protocol, rRNA was removed by using RiboZero kit (Cat No#MRZH11124).
Library was prepared by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7530S)

treatment_protocol: Embryonic stem cells (R1 cells) were harvested after they were grown on feeder cells with LIF, serum and 2i inhibitors till 50-60% confluency, undifferentiated mammary epithelial cells (HC11) were grown till they reach confluency in presence of EGF and Insulin, where as primed cells were harvested after treatment with hydrocortisone along with insulin and were grown for 48 hours prior to RNA isolation. Prolactin stage cells were harvested 72 hours after the primed cells were treated with fresh medium containing hydrocortisone, insulin and prolactin.

tag: strain

value: COMMA-1D Mouse (Balb/c)

value: Mammary Epithelial cells

value: wild type


title: Prolactin HC11  Rep 1 (PRL)


title: Rev-erbα ZT22 rep1


title: icell8 4

description:
Pos_01
RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector


title: icell8 17


title: icell8 5


title: icell8 3


title: Primed HC11 Rep 2 (P)


title: Primed HC11 Rep 1 (P)


title: Sample_OSKM_2c

description: Expression profile of IMR90 + OSKM for 14 days (Rep3)

source_name: IMR90 fibroblasts

extract_protocol:
RNA-Seq libraries were prepared following the Smartseq2 protocol (Picelli et al., 2014 Nat Protocols). Cells from a confluent 96-well were lysed in 50 µl lysis buffer. For reverse transcription, 2 µl lysis mix was used.
Nextera XT Library Preparation (Illumina)

treatment_protocol: Cells were transduced with retroviral OSKM expression or control vectors and selected with 400 µg/ml G418. RNA was extracted after 14 or 20 days.

value: IMR90 fibroblasts

tag: passage

value: OSKM expression

value: 14 days post-transduction


title: icell8 1

value: IMR90 fibroblast


title: Sample_OSKM_2b

description: Expression profile of IMR90 + OSKM for 14 days (Rep2)


title: icell8 6

value: OSKM + shRNA library


title: icell8 7

description:
Neg_02
H2O was used as input

value: no cell

value: no vector


title: icell8 14


title: Normal HC11 Rep 2 (N)


title: Embryonic Stem cells Rep 1

source_name: Mouse R1 cell line

value: Strain 129*1 * 129S1 Mouse

value: Embryonic Stem cells


title: icell8 9


title: Sample_OSKM_2a

description: Expression profile of IMR90 + OSKM for 14 days (Rep1)


title: Sample_OSKM_1c

description: Expression profile of IMR90 + OSKM for 20 days (Rep3)

value: 20 days post-transduction


title: Sample_OSKM_1a

description: Expression profile of IMR90 + OSKM for 20 days (Rep1)


title: Sample_EV_2a

description: Expression profile of IMR90 + control vector for 14 days (Rep1)

value: control


title: Normal HC11 Rep 1 (N)


title: Sample_EV_2c

description: Expression profile of IMR90 + control vector for 14 days (Rep3)


title: Sample_EV_2b

description: Expression profile of IMR90 + control vector for 14 days (Rep2)


title: icell8 44


title: icell8 28

value: K562 myeloid leukemia


title: Sample_EV_1c

description: Expression profile of IMR90 + control vector for 20 days (Rep3)


title: Sample_EV_1b

description: Expression profile of IMR90 + control vector for 20 days (Rep2)


title: Sample_EV_1a

description: Expression profile of IMR90 + control vector for 20 days (Rep1)


title: Embryonic Stem cells Rep 2


title: Sample_OSKM_1b

description: Expression profile of IMR90 + OSKM for 20 days (Rep2)


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; mock treated; biological replicate clone 1

city: New York

first: Jorg

last: Calis

state: NEW YORK

address: 1230 York Avenue

institute: The Rockefeller University

description: CRISPR/CAS9 genome engineering derived cell clone

data_processing:
Paired end reads were mapped with Tophat2 (version 2.0.14).
Read mapping and alignment filtering workflows included several features intended to facilitate identification of RNA editing sites. RNA-Seq read pairs were mapped to human whole-genome reference sequence (GRCh37) supplemented with splice-junction information from Ensembl (version 75) transcript annotations. Relatively permissive read:reference mismatch parameters (--read-mismatches 15; --read-edit-dist 15) were selected to enable mapping of reads potentially derived from transcripts with multiple editing sites.
Only mapped, concordant read pairs were included in downstream RNA editing and gene expression analyses. Read pairs were defined as concordant when both mates mapped to an exonic sequence of the same transcript, or when spanning a genomic sequence smaller than 5000 nucleotides. Concordant read pair alignments with a minimum total matepair read:reference distance from the reference sequence were identified, and selected only if a unique concordant alignment was found.
Gene-level read counts were quantified using htseq-count (version 0.6.1) based on Ensembl (version 75) reference transcriptome annotation.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include sample specific read counts per gene.

source_name: HEK 293T cells

growth_protocol: All cells were grown in DMEM complete media

extract_protocol:
RNA was extracted with the Direct-zol™ RNA MiniPrep (Zymo Research).
Libraries were prepared with the TruSeq Stranded Total RNA with Ribozero kit (Illumina) using 1ug RNA/sample. The ERCC RNA Spike-In Mix (Thermo Fisher Scientific) was added to each RNA sample to achieve a standard measure for gene expression. Two modifications were applied to the standard kit protocol in order to generate libraries with long fragments. First, RNA was fragmented at 94°C for 2 minutes. Second, after ligating adaptors, the volume of AMPure XP Beads (Beckman Coulter) used was reduced to 60% of the suggested volume in the protocol.

treatment_protocol: Samples were mock or IFNb (1nM) treated for 24 hours.

tag: agent

value: mock

value: embryo

value: kidney

value: ADAR1p150 KO


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; mock treated; biological replicate clone 2


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 3

value: Interferon beta


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; mock treated; biological replicate clone 3


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 2


title: RNA-seq of ADAR1p150KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 1


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 1

value: ADAR1 KO


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; mock treated; biological replicate clone 2


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; mock treated; biological replicate clone 1


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 3


title: RNA-seq of Wildtype HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 2

value: wildtype


title: RNA-seq of Wildtype HEK293T cells cultured from clone; mock treated; biological replicate clone 2


title: ZF3_scGSTLT

description: inDrops scGESTALT library for ZF3

source_name: zebrafish brain

extract_protocol:
Single-cell suspensions were processed through inDrops to generate single-cell cDNA libraries. cDNAs were in vitro transcribed, reverse transcribed and prepared for sequencing
Gestalt barcode was PCR amplified by two-step PCR. Sample indices and flow cell adaptors were then added by PCR.

value: brain


title: RNA-seq of Wildtype HEK293T cells cultured from clone; mock treated; biological replicate clone 1


title: RNA-seq of Wildtype HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 3


title: control immunoprecipitation

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

data_processing:
The fastq files were aligned to the S. pombe reference genome ASM294v2 using the STAR aligner (v 2.5.2b) with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. The corresponding reference annotation gtf file was manually curated for snu4 using coordinates II:467,488-467,615.
A counts table for unambiguous uniquely mapped reads was generated using a custom R script.
The read counts for each gene were normalized to the median read counts per library.  Genes were called enriched if the normalized counts in the IP sample exceeded the corresponding counts in the control by 10 or more and the normalized read count ratio was greater than two.
Genome_build: S. pombe ASM294v2
Supplementary_files_format_and_content: STAR_lsm8_all_genes.ignore_strand.SNU4EDIT.tsv; normalized gene counts per sample and enrichment value per gene in tab separated file.

organism: Schizosaccharomyces pombe

source_name: immunoprecipitation

extract_protocol:
Phenol Chloroform extraction
RNA libraries from Lsm8 and control immunoprecipitations were prepared following instructions for Solexa mRNA sequencing and each sample was sequenced on a single lane of the Illumina GAIIx sequencer producing 40bp single-end unstranded reads.

tag: ip


title: ZF1_scGSTLT

description: inDrops scGESTALT library for ZF1


title: imb_beli_2017_06_06_NMS_3

status: Public on Feb 08 2018

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

data_processing:
Sequenced reads were mapped to hg19 genome and ERCC reference sequences using star  v2.5.2b with parameters --outSJfilterReads Unique --outFilterMismatchNmax 2 --outFilterMultimapNmax 10 --alignIntronMin 21 --sjdbOverhang 158 –clip3pAdapterSeq AGATCGGAAGAG
Read counts per gene were generated using featureCounts v1.5.1 with parameter -s 2
Differentially expressed genes were determined using DESeq2 v1.16.1 with ERCC spike-in controls for normalization
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file includes the RPKM values for each sample

source_name: Human osteosarcoma cells

growth_protocol: Human osteosarcoma cells (U2OS) were obtained from ATCC and cultured in D-MEM medium supplemented with 10% fetal bovine serum, L-glutamine, penicillin and streptomycin. All cells were cultured at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
RNA was extracted using the Rneasy Plus Mini Kit (Qiagen). The extraction was performed according to the manufacturer's protocol followed by an additional round starting with the gDNA elimination to improve RNA quality.
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 6 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Midoutput Flowcell, Single Read for 1x 159 cycles plus 7 cycles for the index read.

treatment_protocol: Cells were treated for 4h either with 0.05% DMSO or 5µM NMS-873 (disolved in DMSO)

value: Human osteosarcoma cells


title: imb_beli_2017_06_05_DMSO_3


title: imb_beli_2017_06_01_DMSO_1


title: imb_beli_2017_06_03_DMSO_2


title: Lsm8 immunoprecipitation

description: STAR_lsm8_all_genes.ignore_strand.SNU4EDIT.tsv


title: RNA-seq of Wildtype HEK293T cells cultured from clone; mock treated; biological replicate clone 3


title: RNA-seq of Wildtype HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 1


title: imb_beli_2017_01_13_unt_POL2_2_S13

description: Pol II (N-20), Santa Cruz

data_processing:
NextSeq 500, Basecalling was done with bcl2fastq2 (2.18)
Reads were mapped against GRch37 using bowtie2 (v.2.2.9)
library sized normalised bigwig tracks were produced with extending the reads to fragments using deeptools (v.2.4.2)
Genome_build: GRCh37
Supplementary_files_format_and_content: normalised bigwig tracks

source_name: Human osteosarcoma cell line

growth_protocol: U2OS cells were obtained from ATCC and cultured in D-MEM medium supplemented with 10% fetal bovine serum, L-glutamine, penicillin and streptomycin.

extract_protocol:
ChIP was done according to the protocol described by Arrigoni et al. Cells (20×107/IP) were cross-linked in growth medium containing 1% formaldehyde for 5 min at room temperature, neutralized with 0.125 M glycine and washed twice with PBS. Cell pellet was resuspened in Farnham buffer (FB; 5 mM PIPES pH 8.0, 85 mM KCl, 0.5% IGEPAL CA-630) and incubated for 15 min at 4°C with rotation. Cells were sonicated in 1 ml AFA tubes (Covaris, 520080) using a Covaris S220 focused ultrasonicator (Duty factor: 2%, Cycles/burst: 200, Intensity: 2, water temperature 4°C). The sonication has been stopped when more than 70% of nuclei were isolated (240 sec). NEXON-isolated nuclei were washed twice with FB and resuspended in 1 ml shearing buffer (10 mM Tris-HCl pH 8.0, 0.1% SDS, 1 mM EDTA) supplemented with inhibitors and sheared for 7 min to a fragment size distribution of 100–800 bp (Covaris S220 focused ultrasonicator, Duty factor: 5%; Cycles/burst: 200, Intensity: 4, water temperature 4 °C). 150 µg of precleared chromatin was incubated overnight at 4°C with 5 μg of an antibody followed by 3 hours incubation with 20 µl Dynabeads Protein G (Invitrogen). Beads were washed twice with Wash buffer 1 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-Lauroylsarcosine), twice with Wash buffer 2 (0.25 M LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate, 1 mM EDTA) and the bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. Crosslinks were reversed by incubation at 65°C overnight with gentle shaking. Subsequently, chromatin was incubated with RNase A (0.2 mg/ml) for 30 min at 37°C and then with proteinase K (50 μg/ml) for 3 hours at 55°C. DNA was purified by phenol–chloroform extraction followed by ethanol precipitation and recovered in 30 μl (IP samples) or 50 μl (inputs) RNase free water. Real-time PCR on the ChIP-ed material was performed using SYBR Green (ABI).
ChIP-seq library preparation was performed using NuGEN´s Ovation Ultralow System V2 1-96 (2014). Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 flowcell, PE for 2x 42 cycles plus 8 cycles for the index read.

treatment_protocol: Cells were either mock-treated, irradiated with UV light (40 J/m2, 1 hour recovery) or pre-treated with 10 µM of p38 inhibitor SB203580 (Selleckchem) for 1-hour prior to irradiation with UV light (40 J/m2, 1 hour recovery).

tag: cell type

tag: treatment

value: untreated


title: imb_beli_2017_01_14_uv_POL2_2_S14

description: Pol II (N-20), Santa Cruz

value: UV


title: imb_beli_2017_01_02_uv_input_1_S2

description: input control


title: imb_beli_2017_01_01_unt_input_1_S1

description: input control


title: imb_beli_2017_01_05_uv_input_2_S5

description: input control


title: imb_beli_2017_01_04_unt_input_2_S4

description: input control


title: imb_beli_2017_01_11_uv_POL2_1_S11

description: Pol II (N-20), Santa Cruz


title: RNA_VitDex_2hr_BR1_TR1

first: Leona

last: Gabrysova

address: 1 Midland Road

institute: The Crick Institute

description: Two sequencing runs performed for this sample.

data_processing:
Alignment of reads to the mouse transcriptome (mm10) and absolute quantification of the genes was performed in Strand NGS (version 2.0), merging files from the different sequencing runs when available, using default parameters (95% identity, max 5% gaps, 1 read only if duplicated, ignoring reads with more than 5 matches) and guided by RefSeq annotations (2013.04.01).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: VitDex,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of Vitamin D3 (4x10-8M, Enzo Life Sciences), Dexamethasone (1x10-8M, Sigma-Aldrich), anti-IFNg (Harlan), anti-IL-12 (gift from Dr. G. Trinchieri) and anti-IL-4 (gift from DNAX) at 10 ug/ml for 21 days with anti-CD3/28 (2 ug/ml) restimulation in the presence of the above on day 7 and day 14. On day 21, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

extract_protocol:
Extraction of total RNA was carried out using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
Libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina) according to the manufacturer’s instructions.

treatment_protocol:
Cultured with Vitamin D3, Dexamethasone, anti-IFNg, anti-IL-12p40, anti-IFNg and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.

value: spleen

value: CD4+ T cell

tag: cd4+ t cell subset

value: VitDex

tag: time point


title: imb_beli_2017_01_10_unt_POL2_1_S10

description: Pol II (N-20), Santa Cruz


title: RNA_VitDex_6hr_BR2_TR1

source_name: VitDex,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of Vitamin D3 (4x10-8M, Enzo Life Sciences), Dexamethasone (1x10-8M, Sigma-Aldrich), anti-IFNg (Harlan), anti-IL-12 (gift from Dr. G. Trinchieri) and anti-IL-4 (gift from DNAX) at 10 ug/ml for 21 days with anti-CD3/28 (2 ug/ml) restimulation in the presence of the above on day 7 and day 14. On day 21, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured with Vitamin D3, Dexamethasone, anti-IFNg, anti-IL-12p40, anti-IFNg and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_VitDex_6hr_BR1_TR1


title: RNA_VitDex_2hr_BR2_TR1


title: imb_beli_2017_06_04_NMS_2


title: RNA_VitDex_0hr_BR2_TR1

source_name: VitDex,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of Vitamin D3 (4x10-8M, Enzo Life Sciences), Dexamethasone (1x10-8M, Sigma-Aldrich), anti-IFNg (Harlan), anti-IL-12 (gift from Dr. G. Trinchieri) and anti-IL-4 (gift from DNAX) at 10 ug/ml for 21 days with anti-CD3/28 (2 ug/ml) restimulation in the presence of the above on day 7 and day 14.

treatment_protocol:
Cultured with Vitamin D3, Dexamethasone, anti-IFNg, anti-IL-12p40, anti-IFNg and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_VitDex_0.5hr_BR1_TR1

source_name: VitDex,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of Vitamin D3 (4x10-8M, Enzo Life Sciences), Dexamethasone (1x10-8M, Sigma-Aldrich), anti-IFNg (Harlan), anti-IL-12 (gift from Dr. G. Trinchieri) and anti-IL-4 (gift from DNAX) at 10 ug/ml for 21 days with anti-CD3/28 (2 ug/ml) restimulation in the presence of the above on day 7 and day 14. On day 21, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured with Vitamin D3, Dexamethasone, anti-IFNg, anti-IL-12p40, anti-IFNg and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_VitDex_0.5hr_BR2_TR1


title: RNA_VitDex_0hr_BR1_TR1


title: RNA_TH2_6hr_BR2_TR1

source_name: TH2,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-4 (10 ng/ml, R&D Systems), IL-2 (5 ng/ml, Insight Biotechnology), anti-IL-12p40 and anti-IFNg (10 ug/ml, gift from Dr. G. Trichieri and DNAX, respectively). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured with IL-4, IL-2, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH2_2hr_BR2_TR1

source_name: TH2,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-4 (10 ng/ml, R&D Systems), IL-2 (5 ng/ml, Insight Biotechnology), anti-IL-12p40 and anti-IFNg (10 ug/ml, gift from Dr. G. Trichieri and DNAX, respectively). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

treatment_protocol:
Cultured with IL-4, IL-2, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH2_0hr_BR1_TR1

source_name: TH2,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-4 (10 ng/ml, R&D Systems), IL-2 (5 ng/ml, Insight Biotechnology), anti-IL-12p40 and anti-IFNg (10 ug/ml, gift from Dr. G. Trichieri and DNAX, respectively) for 7 days.

treatment_protocol:
Cultured with IL-4, IL-2, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH2_2hr_BR1_TR1


title: RNA_TH2_0hr_BR2_TR1


title: RNA_TH2_6hr_BR1_TR1


title: RNA_TH2_0.5hr_BR2_TR1

source_name: TH2,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-4 (10 ng/ml, R&D Systems), IL-2 (5 ng/ml, Insight Biotechnology), anti-IL-12p40 and anti-IFNg (10 ug/ml, gift from Dr. G. Trichieri and DNAX, respectively). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured with IL-4, IL-2, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1IL27_6hr_BR2_TR1

source_name: TH1IL27,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend), IL-27 20ng/ml (R&D Systems) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured with IL-12p70, IL-27 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1IL27_6hr_BR1_TR1


title: RNA_TH1IL27_2hr_BR2_TR1


title: RNA_TH1IL27_2hr_BR1_TR1

source_name: TH1IL27,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend), IL-27 20ng/ml (R&D Systems) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

treatment_protocol:
Cultured with IL-12p70, IL-27 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH2_0.5hr_BR1_TR1


title: RNA_TH17_6hr_BR2_TR3

source_name: TH17,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (2 ug/ml) and anti-CD28 (10 ug/ml) and cultured in IMDM in the presence of rhTGFb1 (2 ng/ml, R&D Systems), rhIL-6 (50 ng/ml, R&D Systems), anti-IL-12 (gift from Dr. G. Trichieri), anti-IFNg (Harlan) and anti-IL-4 (gift from DNAX) at 10ng/ml. On day 5, cells were harvested and restimulated with PDBU (Sigma-Aldrich) and Ionomycin (Calbiochem) at 500 ng/ml for 6h.

treatment_protocol:
Cultured with IL-6, TGFb1, anti-IL-12p70, anti-IFNg and anti-IL-4 for 5d, re-stimulated with PMA and Ionomycin for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH17_6hr_BR2_TR2


title: RNA_TH17_6hr_BR2_TR1


title: RNA_TH17_6hr_BR1_TR1


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; mock treated; biological replicate clone 3


title: RNA_TH1IL27_0hr_BR2_TR1

source_name: TH1IL27,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend), IL-27 20ng/ml (R&D Systems) and anti-IL-4 (10 ug/ml, gift from DNAX) for 7 days.

treatment_protocol:
Cultured with IL-12p70, IL-27 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH17_6hr_BR1_TR3


title: RNA_TH17_6hr_BR1_TR2


title: RNA_TH17_2hr_BR2_TR3

source_name: TH17,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (2 ug/ml) and anti-CD28 (10 ug/ml) and cultured in IMDM in the presence of rhTGFb1 (2 ng/ml, R&D Systems), rhIL-6 (50 ng/ml, R&D Systems), anti-IL-12 (gift from Dr. G. Trichieri), anti-IFNg (Harlan) and anti-IL-4 (gift from DNAX) at 10ng/ml. On day 5, cells were harvested and restimulated with PDBU (Sigma-Aldrich) and Ionomycin (Calbiochem) at 500 ng/ml for 2h.

treatment_protocol:
Cultured with IL-6, TGFb1, anti-IL-12p70, anti-IFNg and anti-IL-4 for 5d, re-stimulated with PMA and Ionomycin for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1IL27_0.5hr_BR2_TR1

source_name: TH1IL27,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend), IL-27 20ng/ml (R&D Systems) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured with IL-12p70, IL-27 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH17_2hr_BR2_TR2


title: RNA_TH17_2hr_BR1_TR2


title: RNA_TH1IL27_0hr_BR1_TR1


title: RNA_TH17_2hr_BR1_TR3


title: RNA_TH17_2hr_BR2_TR1


title: RNA_TH1IL27_0.5hr_BR1_TR1


title: RNA_TH17_2hr_BR1_TR1


title: RNA_TH17_0hr_BR2_TR3

source_name: TH17,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (2 ug/ml) and anti-CD28 (10 ug/ml) and cultured in IMDM in the presence of rhTGFb1 (2 ng/ml, R&D Systems), rhIL-6 (50 ng/ml, R&D Systems), anti-IL-12 (gift from Dr. G. Trichieri), anti-IFNg (Harlan) and anti-IL-4 (gift from DNAX) at 10ng/ml for 5 days.

treatment_protocol:
Cultured with IL-6, TGFb1, anti-IL-12p70, anti-IFNg and anti-IL-4 for 5d, re-stimulated with PDBU and Ionomycin for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH17_0hr_BR2_TR1


title: RNA_TH17_0hr_BR1_TR2


title: RNA_TH17_0hr_BR1_TR1


title: RNA_TH17_0hr_BR2_TR2


title: RNA_TH17_0.5hr_BR2_TR2

source_name: TH17,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (2 ug/ml) and anti-CD28 (10 ug/ml) and cultured in IMDM in the presence of rhTGFb1 (2 ng/ml, R&D Systems), rhIL-6 (50 ng/ml, R&D Systems), anti-IL-12 (gift from Dr. G. Trichieri), anti-IFNg (Harlan) and anti-IL-4 (gift from DNAX) at 10ng/ml. On day 5, cells were harvested and restimulated with PDBU (Sigma-Aldrich) and Ionomycin (Calbiochem) at 500 ng/ml for 0.5h.

treatment_protocol:
Cultured with IL-6, TGFb1, anti-IL-12p70, anti-IFNg and anti-IL-4 for 5d, re-stimulated with PMA and Ionomycin for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH17_0.5hr_BR2_TR1


title: RNA_TH17_0.5hr_BR1_TR3


title: RNA_TH17_0.5hr_BR1_TR1


title: RNA_TH1_6hr_BR1_TR1

source_name: TH1,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured with IL-12p70 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1_0hr_BR2_TR1

source_name: TH1,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend) and anti-IL-4 (10 ug/ml, gift from DNAX) for 7 days.

treatment_protocol:
Cultured with IL-12p70 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1_2hr_BR1_TR1

source_name: TH1,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

treatment_protocol:
Cultured with IL-12p70 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1_0hr_BR1_TR1


title: imb_beli_2017_06_02_NMS_1

source_name: Human osteosarcoma cells

growth_protocol: Human osteosarcoma cells (U2OS) were obtained from ATCC and cultured in D-MEM medium supplemented with 10% fetal bovine serum, L-glutamine, penicillin and streptomycin. All cells were cultured at 37 °C in a humidified incubator at 5% CO2.

treatment_protocol: Cells were treated for 4h either with 0.05% DMSO or 5µM NMS-873 (disolved in DMSO)


title: RNA_TH1_6hr_BR2_TR1


title: RNA_TH1_2hr_BR2_TR1


title: RNA_TH17_0.5hr_BR1_TR2


title: RNA_TH17_0hr_BR1_TR3


title: RNA_TH0block_6hr_BR2_TR1

source_name: TH0block,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of anti-IL-4, anti-IL-6, anti-TGFb (gifts from DNAX), anti-IL-12p40 (gift from Dr. G. Trinchieri) and anti-IFNg (Harlan) at 10 ug/ml for 7 days. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured with anti-IL-4, anti-IL-6, anti-TGFb, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1_0.5hr_BR2_TR1

source_name: TH1,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of rmIL-12p70 (5 ng/ml, Biolegend) and anti-IL-4 (10 ug/ml, gift from DNAX). On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured with IL-12p70 and anti-IL-4 for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0block_2hr_BR2_TR1

source_name: TH0block,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of anti-IL-4, anti-IL-6, anti-TGFb (gifts from DNAX), anti-IL-12p40 (gift from Dr. G. Trinchieri) and anti-IFNg (Harlan) at 10 ug/ml for 7 days. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

treatment_protocol:
Cultured with anti-IL-4, anti-IL-6, anti-TGFb, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH1_0.5hr_BR1_TR1


title: RNA_TH17_0.5hr_BR2_TR3


title: RNA_TH0block_0.5hr_BR2_TR1

source_name: TH0block,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of anti-IL-4, anti-IL-6, anti-TGFb (gifts from DNAX), anti-IL-12p40 (gift from Dr. G. Trinchieri) and anti-IFNg (Harlan) at 10 ug/ml for 7 days. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured with anti-IL-4, anti-IL-6, anti-TGFb, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0block_2hr_BR1_TR1


title: RNA_TH0block_6hr_BR1_TR1


title: RNA_TH0block_0.5hr_BR1_TR1


title: RNA_TH0_6hr_BR2_TR3

source_name: TH0,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 6h.

treatment_protocol:
Cultured for 7d, re-stimulated with anti-CD3/CD28 for 6h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0_6hr_BR2_TR2


title: RNA_TH0block_0hr_BR1_TR1

source_name: TH0block,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI in the presence of anti-IL-4, anti-IL-6, anti-TGFb (gifts from DNAX), anti-IL-12p40 (gift from Dr. G. Trinchieri) and anti-IFNg (Harlan) at 10 ug/ml for 7 days.

treatment_protocol:
Cultured with anti-IL-4, anti-IL-6, anti-TGFb, anti-IL-12p40 and anti-IFNg for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0_6hr_BR2_TR1


title: RNA_TH0_6hr_BR1_TR3


title: RNA_TH0_2hr_BR2_TR3

source_name: TH0,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 2h.

treatment_protocol:
Cultured for 7d, re-stimulated with anti-CD3/CD28 for 2h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0_6hr_BR1_TR1


title: RNA_TH0_6hr_BR1_TR2


title: RNA_TH0_2hr_BR2_TR2


title: RNA_TH0_2hr_BR2_TR1


title: RNA_TH0_0hr_BR2_TR2

source_name: TH0,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI for 7 days.

treatment_protocol:
Cultured for 7d, re-stimulated with anti-CD3/CD28 for 0h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0_2hr_BR1_TR3


title: RNA_TH0block_0hr_BR2_TR1


title: RNA_TH0_2hr_BR1_TR2


title: RNA_TH0_0hr_BR2_TR1


title: RNA_TH0_0hr_BR1_TR3


title: RNA_TH0_0hr_BR1_TR2


title: RNA_TH0_2hr_BR1_TR1


title: RNA_TH0_0hr_BR1_TR1


title: RNA_TH0_0.5hr_BR2_TR2

source_name: TH0,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI. On day 7, cells were harvested and restimulated with anti-CD3 (2 ug/ml) and anti-CD28 (2ug/ml) for 0.5h.

treatment_protocol:
Cultured for 7d, re-stimulated with anti-CD3/CD28 for 0.5h.
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_TH0_0.5hr_BR1_TR2


title: RNA_Naive_2hr_BR2_TR2

source_name: Naive,2hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI for 2h.

treatment_protocol:
None, cells were cultured for 2h
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.

value: Naive


title: RNA_TH0_0.5hr_BR1_TR3


title: RNA_TH0_0hr_BR2_TR3


title: RNA_Naive_2hr_BR2_TR3


title: RNA_Naive_6hr_BR2_TR2

source_name: Naive,6hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti- CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI for 6h.

treatment_protocol:
None, cells were cultured for 6h
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_Naive_6hr_BR2_TR3


title: RNA_Naive_6hr_BR1_TR1


title: RNA_Naive_2hr_BR2_TR1


title: RNA_TH0_0.5hr_BR1_TR1


title: RNA_Naive_6hr_BR2_TR1


title: RNA_Naive_0hr_BR2_TR3

source_name: Naive,0hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter).

treatment_protocol:
None
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_Naive_2hr_BR1_TR1


title: RNA_Naive_0hr_BR2_TR2


title: RNA_TH0_0.5hr_BR2_TR3


title: RNA_TH0_0.5hr_BR2_TR1


title: RNA_Naive_0hr_BR1_TR1


title: RNA_Naive_0.5hr_BR2_TR1

source_name: Naive,0.5hr,in vitro

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti- anti-CD8-FITC, anti-CD4-eFluor450, anti-CD25-APC, anti-CD62L-PECy7, anti-CD44-PE (eBioscience). Live (propidium iodide negative) CD8-CD4+CD25-CD62L+CD44lo T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter). Sorted cells were activated with anti-CD3 (5 ug/ml) and anti-CD28 (2 ug/ml) and cultured in RPMI for 0.5h.

treatment_protocol:
None, cells were cultured for 0.5h
CD4+ T cells were differentiated as described where biological replicates [BR] refer to different experiment, technical replicates [TR] are different culture wells within the same biological replicate. Some samples were sequenced in two runs. These samples are identified in the 'description' field and include two SRR per sample.


title: RNA_Foxp3IL10pos_0hr_BR2_TR1

source_name: Foxp3IL10pos,0hr,ex vivo

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD4-APCeFluor780 (eBioscience). Live (LIVE/DEAE Fixable Violet negative) CD4+Foxp3RFP+IL-10+ were sorted on a MoFloTM XDP cytometer (Beckman Coulter).

value: Foxp3RFP IL-10GFP dual reporter mice

value: CD4+ T cell (Treg)


title: RNA_Naive_0.5hr_BR2_TR3


title: RNA_Naive_0.5hr_BR2_TR2


title: RNA_Naive_0.5hr_BR1_TR1


title: RNA_Foxp3IL10pos_0hr_BR3_TR1


title: RNA_Foxp3IL10neg_0hr_BR3_TR1

source_name: Foxp3IL10neg,0hr,ex vivo

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD4-APCeFluor780 (eBioscience). Live (LIVE/DEAE Fixable Violet negative) CD4+Foxp3RFP+IL-10- were sorted on a MoFloTM XDP cytometer (Beckman Coulter).


title: RNA_Foxp3IL10neg_0hr_BR2_TR1


title: RNA_Foxp3IL10neg_0hr_BR1_TR1


title: RNA_UNT_cMaf_flfl_3

data_processing:
Alignment of reads to the mouse transcriptome (mm10) and absolute quantification of the genes was performed in Strand NGS (version 2.0) with default parameters (95% identity, max 5% gaps, 1 read only if duplicated, ignoring reads with more than 5 matches) guided by Ensembl (2014.04.01) annotations.
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided for RNA-seq data normalised to RPKMs

source_name: CD4+ T cells (untreated)

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD4-eFluor450 and anti-CD8 FITC (eBioscience). Live (propidium iodide negative) CD3+CD8-CD4+ T cells were sorted using on a MoFloTM XDP (Beckman Coulter) or BD Fusion cytometers.

value: c-Maf flfl

value: Spleen


title: RNA_Foxp3IL10pos_0hr_BR1_TR1


title: RNA_UNT_cMaf_flfl_2


title: RNA_MAL_cMaf_flfl_1

source_name: CD4+ T cells (Th1 malaria model)

growth_protocol: On day 7 post infection, CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD4-eFluor450, anti-CD8 FITC (eBioscience) and anti-Ter119-APCCy7 (BD). Live (propidium iodide negative) Ter119-CD3+CD8-CD4+ T cells were sorted using on a MoFloTM XDP (Beckman Coulter) or BD Fusion cytometers.

treatment_protocol: c-Maf flfl mice were infected with 105 Plasmodim chabaudi chabaudi AS infected red blood cells on day 0.

value: day 7 post Plasmodim chabaudi chabaudi AS infection


title: RNA_HDM_cMaf_flfl_CD4Cre_2

source_name: CD4+ T cells (Th2 HDM allergy model)

growth_protocol: On day 25, CD4+ T cells were enriched from perfused lungs (pooled) following a Percoll gradient separation by positive selection using anti-CD4 microbeads (Miltenyi Biotech). After staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD8 FITC, anti-CD4-eFluor450 and anti-CD44-PE (eBioscience), CD3+CD8-CD4+CD44+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer.

treatment_protocol: c-Maf flfl CD4Cre mice were sensitized with 10 mg HDM (Greer) or PBS and 2mg Imject Alum (Thermo Scientific) by intraperitoneal injections on days 0 and 14, and challenged intratracheally with 10 mg HDM or PBS on days 21 and 24.

value: c-Maf flfl CD4Cre

value: Lung

value: day 25 of HDM induced allergy


title: RNA_MAL_cMaf_flfl_3


title: RNA_MAL_cMaf_flfl_CD4Cre_3

treatment_protocol: c-Maf flfl CD4Cre mice were infected with 105 Plasmodim chabaudi chabaudi AS infected red blood cells on day 0.


title: RNA_HDM_cMaf_flfl_CD4Cre_3


title: RNA_Naive_0hr_BR2_TR1

value: wildtype


title: RNA_UNT_cMaf_flfl_1


title: RNA_HDM_cMaf_flfl_1

treatment_protocol: c-Maf flfl mice were sensitized with 10 mg HDM (Greer) or PBS and 2mg Imject Alum (Thermo Scientific) by intraperitoneal injections on days 0 and 14, and challenged intratracheally with 10 mg HDM or PBS on days 21 and 24.


title: RNA_EAE_cMaf_flfl_CD4Cre_3

source_name: CD4+ T cells (Th17 EAE model)

growth_protocol: On day 14-16, CD4+ T cells were isolated from brains and spinal cords (pooled) following a Percoll gradient separation and staining in PBS with 5% FCS for 20 min at 4C with anti-CD45.2-PE, anti-CD11b-FITC, anti-CD3-APC and anti-CD4-eFluor450. CD8-CD45.2+CD3+CD4+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer.

treatment_protocol: c-Maf flfl CD4Cre mice were immunised subcutaneously with 250 ug MOG35-55 peptide (Cambridge Research Biochemicals) emulsified in complete Freund’s adjuvant containing 250 ug heat-killed M. tuberculosis H37RA (Difco Laboratories) on day 0. On days 0 and 2 post immunisation, mice received 200ng pertussis toxin (Calbiochem) intraperitoneally.

value: CNS (brain and spinal cord)

value: day 14-16 post EAE induction


title: RNA_HDM_cMaf_flfl_3


title: RNA_HDM_cMaf_flfl_2


title: RNA_EAE_cMaf_flfl_CD4Cre_2


title: RNA_EAE_cMaf_flfl_CD4Cre_1


title: RNA_EAE_cMaf_flfl_2

growth_protocol: On day 14-16, CD4+ T cells were isolated from brains and spinal cords (pooled) following a Percoll gradient separation and staining in PBS with 5% FCS for 20 min at 4C with anti-CD45.2-PE, anti-CD11b-FITC, anti-CD3-APC and anti-CD4-eFluor450. CD8-CD45.2+CD3+CD4+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer

treatment_protocol: c-Maf flfl mice were immunised subcutaneously with 250 ug MOG35-55 peptide (Cambridge Research Biochemicals) emulsified in complete Freund’s adjuvant containing 250 ug heat-killed M. tuberculosis H37RA (Difco Laboratories) on day 0. On days 0 and 2 post immunisation, mice received 200ng pertussis toxin (Calbiochem) intraperitoneally.


title: ATAC_EAE_cMaf_flfl _CD4Cre_1

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 with BWA-MEM
Duplicates were removed using Picard
alignment QC, discarded alignments with a mapQ below 30 using SAMtools 1.3.1
Discarded alignemnts done to mitochondrial DNA, shifted Reads to represent the Tn5 insertion, and remove fragments spanning nucleosomes (size >99 bp) using awk and BEDTools 2.4.2. Fragments spanning nucleosomes were not removed for the one untreated sample
MACS2 2.1.1 (parameters --keep-dup all, --nomodel, --shift -100, --extsize 200) was used to call peaks (q-value < 0.01)
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided for ATAC-seq data normalised to RPKMs (fragments spanning nucleosomes excluded), for peaks called bed files are provided

extract_protocol: Cells sorting was followed by a transposition reaction and purification, prepared as in Buenrostro et al. Curr Protoc Mol Biol. 2015 with the transposition reaction carried out for 1h and 30 minutes at 37 °C and subsequent PCR amplification for 12 cycles


title: RNA_EAE_cMaf_flfl_3


title: RNA_EAE_cMaf_flfl_1


title: ATAC_EAE_cMaf_flfl _CD4Cre_2


title: ZF2_scGSTLT

description: inDrops scGESTALT library for ZF2

source_name: zebrafish brain

value: brain


title: ATAC_EAE_cMaf_flfl _CD4Cre_3


title: ATAC_EAE_cMaf_flfl _2


title: RNA_MAL_cMaf_flfl_CD4Cre_2


title: RNA_MAL_cMaf_flfl_CD4Cre_1


title: RNA_MAL_cMaf_flfl_2


title: ATAC_EAE_cMaf_flfl _1


title: ATAC_HDM_cMaf_flfl _CD4Cre_1

growth_protocol: On day 25, CD4+ T cells were enriched from perfused lungs (pooled) following a Percoll gradient separation by positive selection using anti-CD4 microbeads (Miltenyi Biotech). After staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD8 FITC, anti-CD4-eFluor450 and and anti-CD44-PE (eBioscience), CD3+CD8-CD4+CD44+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer.


title: ATAC_HDM_cMaf_flfl _CD4Cre_3


title: ATAC_MAL_cMaf_flfl _CD4Cre_3

growth_protocol: On day 7 post infection, CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD4-eFluor450, anti-CD3-APC (eBioscience) and anti-Ter119-APCCy7 (BD). Live (propidium iodide negative) Ter119-CD3+CD4+ T cells were sorted using on a MoFloTM XDP (Beckman Coulter) or BD Fusion cytometers.


title: ATAC_HDM_cMaf_flfl _CD4Cre_2


title: ATAC_HDM_cMaf_flfl_2


title: ATAC_HDM_cMaf_flfl_3


title: RNA_HDM_cMaf_flfl_CD4Cre_1


title: ATAC_MAL_cMaf_flfl _CD4Cre_1


title: ATAC_MAL_cMaf_flfl_2


title: ATAC_MAL_cMaf_flfl_1


title: RNA-seq of ADAR1KO HEK293T cells cultured from clone; Interferon beta treated; biological replicate clone 2

source_name: HEK 293T cells

growth_protocol: All cells were grown in DMEM complete media

treatment_protocol: Samples were mock or IFNb (1nM) treated for 24 hours.

value: Interferon beta

value: embryo

value: kidney

value: ADAR1 KO


title: ATAC_MAL_cMaf_flfl_3

value: CD4+ T cell


title: ATAC_UNT_C57BL6 1

source_name: CD4+ T cells from untreated WT mice

growth_protocol: CD4+ T cells were negatively enriched from spleen using goat anti-MHCII, anti-CD8 and anti-B220 and anti-goat beads (Quiagen), followed by staining in PBS with 5% FCS for 20 min at 4C with anti-CD4-eFluor450 and anti-CD8-FITC (eBioscience). Live (propidium iodide negative) CD4+CD8- T cells were sorted on a MoFloTM XDP cytometer (Beckman Coulter).


title: highfat_smRNA4

city: West Lafayette

first: Theresa

middle: M

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

institute: Purdue University

description:
highfat diet
Sample name: HF71

data_processing:
Raw Sequenced reads were trimmed for the adaptor sequence, followed by the clipping of 4 bases from either ends (as specified by  the Bioo Scientific kit “NEXTflex Illumina Small RNA Sequencing Kit v3”) and quality trimming through cutadapt software version 1.9.1
Preprocessing of trimmed reads through the mapper.pl script from miRDeep2 which performs steps such as adapter clipping, discarding the reads shorter than 18 bp and reads collapsing.
Quantification and expression profiling of known miRNA was performed by the quantifier.pl script from miRDeep2 using the collapsed reads and miRBase database as a reference.
The quantifier script generated the read counts against the known miRNAs from each sample.
The read counts from the different sample were collated using the custom scripts to generate a single file representing the read counts against known miRNA from all the samples.
Genome_build: Mus musculus GRCm38 (Release 85) downloaded from Ensembl website. Mus musculus miRNAs (Release 21) downloaded from the miRBase website.
Supplementary_files_format_and_content: Tab delimited text file containing read counts for each known miRNA from each sample.

source_name: milk fat

extract_protocol:
Milk fat layer was isolated by centrifugation (1000-g for 5 min) at 4 °C from lactation day 10 samples, and transferred to a new microfuge.  An equal volume of PBS was added and mixed with milk fat by vortexing. Milk-fat PBS mixture was centrifuged for 5 min in 4 °C at 3000 rpm to remove cells and other debris that may have been trapped in fat. The miRNeasy Mini Kit (cat. No. 217004, company: QIAGEN) was used to isolate total RNA following manufacturer’s directions using these specifications; Lysis Reagent was added to sample at a 1:3.5 ratio (200ul milk sample to 700ul QIAzol) followed by disruption and homogenization using vortex. Total RNA was eluted from final column with 20 µl of RNase-Free water and stored at -80° C, until sequencing.
NEXTflexTM –Small RNA-Seq Kit v3 (Bioo Scientific) was used to generate small RNA libraries directly from total RNA. Libraries were sequenced on an Illumina HiSeq2500 platform

treatment_protocol: Nine 4-week old female ICR (CD1; Envigo) mice were matched by weight and divided into two treatment groups: control (n=5) and high fat (HF; n=4) diet. Mice were exposed to a 12h light: 12h dark cycle throughout entire study.  For the 4 weeks prior to mating, female mice were housed in pairs within treatment and fed a high fat diet (HF; Research Diets #D12492, 60% of total kcal energy is fat and 7% of total kcal is sucrose; 5.24kcal/gm; Brunswick, NJ) or control diet that was matched for sucrose (C; Research Diets #D12450J, 10% of total kcal energy is fat and  7% of total kcal is sucrose; 3.85 kcal/gm). Dams remained on respective diets throughout pregnancy and lactation. Milk was collected from each dam on post-natal day 10.

tag: biological replicate

value: milk fat

value: ICR

tag: age

value: primiparous

value: lactation day 10

tag: Sex

value: female


title: ATAC_MAL_cMaf_flfl _CD4Cre_2

value: c-Maf flfl CD4Cre

tag: tissue

value: Spleen

value: day 7 post Plasmodim chabaudi chabaudi AS infection


title: highfat_smRNA3

description:
highfat diet
Sample name: HF70

tag: developmental stage