title: Pancreatic islet cell sample 413

value: Pancreatic islets


title: Pancreatic islet cell sample 409

status: Public on Aug 31 2016

type: SRA

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

country: USA

institute: Regeneron Pharmaceuticals, Inc.

library_source: transcriptomic

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (human: GRCh37) using CLC bio Genomics Workbench Version 7.0 (CLC Bio) allowing one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic islets

extract_protocol:
Single islet cells were captured with C1 Integrated Fluidic Circuit. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Protocol #100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

tag: tissue

tag: donor id

value: Non T2D 10

tag: condition

value: non-diabetic

tag: age

tag: ethnicity

value: C

tag: gender

value: M

tag: cell subtype

value: alpha


title: Pancreatic islet cell sample 411


title: Pancreatic islet cell sample 406

value: Non T2D 9

value: F


title: Pancreatic islet cell sample 404


title: Pancreatic islet cell sample 408


title: Pancreatic islet cell sample 426


title: Pancreatic islet cell sample 405


title: Pancreatic islet cell sample 402


title: Pancreatic islet cell sample 401


title: Pancreatic islet cell sample 400


title: Pancreatic islet cell sample 403


title: Pancreatic islet cell sample 398


title: Pancreatic islet cell sample 396


title: Pancreatic islet cell sample 397


title: Pancreatic islet cell sample 399


title: Pancreatic islet cell sample 395


title: Pancreatic islet cell sample 394


title: Pancreatic islet cell sample 392


title: Pancreatic islet cell sample 391


title: Pancreatic islet cell sample 389


title: Pancreatic islet cell sample 390


title: Pancreatic islet cell sample 410


title: Pancreatic islet cell sample 385


title: Pancreatic islet cell sample 386


title: Pancreatic islet cell sample 387


title: Pancreatic islet cell sample 384


title: Pancreatic islet cell sample 388


title: Pancreatic islet cell sample 380

value: Non T2D 8

value: AI


title: Pancreatic islet cell sample 378


title: Pancreatic islet cell sample 381


title: Pancreatic islet cell sample 382


title: Pancreatic islet cell sample 375


title: Pancreatic islet cell sample 373

value: Non T2D 3


title: Pancreatic islet cell sample 371


title: Pancreatic islet cell sample 370


title: Pancreatic islet cell sample 367


title: Pancreatic islet cell sample 372


title: Pancreatic islet cell sample 369


title: Pancreatic islet cell sample 368


title: Pancreatic islet cell sample 393


title: Pancreatic islet cell sample 379


title: Pancreatic islet cell sample 366


title: Pancreatic islet cell sample 365


title: Pancreatic islet cell sample 363


title: Pancreatic islet cell sample 364


title: Pancreatic islet cell sample 376


title: Pancreatic islet cell sample 362


title: Pancreatic islet cell sample 361


title: Pancreatic islet cell sample 360


title: Pancreatic islet cell sample 357


title: Pancreatic islet cell sample 383


title: Pancreatic islet cell sample 354


title: Pancreatic islet cell sample 356


title: Pancreatic islet cell sample 359


title: Pancreatic islet cell sample 355


title: Pancreatic islet cell sample 353


title: Pancreatic islet cell sample 350


title: Pancreatic islet cell sample 358


title: Pancreatic islet cell sample 352


title: Pancreatic islet cell sample 349


title: Pancreatic islet cell sample 346

value: Non T2D 7


title: Pancreatic islet cell sample 351


title: Pancreatic islet cell sample 342


title: Pancreatic islet cell sample 348


title: Pancreatic islet cell sample 337

value: Non T2D 6


title: Pancreatic islet cell sample 344


title: Pancreatic islet cell sample 347


title: Pancreatic islet cell sample 377


title: Pancreatic islet cell sample 334


title: Pancreatic islet cell sample 340


title: Pancreatic islet cell sample 374


title: Pancreatic islet cell sample 341


title: Pancreatic islet cell sample 339


title: Pancreatic islet cell sample 343


title: Pancreatic islet cell sample 336


title: Pancreatic islet cell sample 338


title: Pancreatic islet cell sample 327


title: Pancreatic islet cell sample 325


title: Pancreatic islet cell sample 326


title: Pancreatic islet cell sample 321


title: Pancreatic islet cell sample 333


title: Pancreatic islet cell sample 320


title: Pancreatic islet cell sample 330


title: Pancreatic islet cell sample 335


title: Pancreatic islet cell sample 332


title: Pancreatic islet cell sample 331


title: Pancreatic islet cell sample 322


title: Pancreatic islet cell sample 328


title: Pancreatic islet cell sample 312


title: Pancreatic islet cell sample 315


title: Pancreatic islet cell sample 316


title: Pancreatic islet cell sample 329


title: Pancreatic islet cell sample 319


title: Pancreatic islet cell sample 313


title: Pancreatic islet cell sample 345


title: Pancreatic islet cell sample 314


title: Pancreatic islet cell sample 308


title: Pancreatic islet cell sample 310


title: Pancreatic islet cell sample 311


title: Pancreatic islet cell sample 323


title: Pancreatic islet cell sample 307


title: Pancreatic islet cell sample 309


title: Pancreatic islet cell sample 324


title: Pancreatic islet cell sample 306


title: Pancreatic islet cell sample 305


title: Pancreatic islet cell sample 304


title: Pancreatic islet cell sample 303


title: Pancreatic islet cell sample 302


title: Pancreatic islet cell sample 301

value: Non T2D 5

value: AA


title: Pancreatic islet cell sample 300


title: Pancreatic islet cell sample 317


title: Pancreatic islet cell sample 297


title: Pancreatic islet cell sample 298


title: Pancreatic islet cell sample 296


title: Pancreatic islet cell sample 299


title: Pancreatic islet cell sample 289


title: Pancreatic islet cell sample 288


title: Pancreatic islet cell sample 292


title: Pancreatic islet cell sample 290


title: Pancreatic islet cell sample 287


title: Pancreatic islet cell sample 291


title: Pancreatic islet cell sample 285


title: Pancreatic islet cell sample 286


title: Pancreatic islet cell sample 284


title: Pancreatic islet cell sample 283


title: Pancreatic islet cell sample 282


title: Pancreatic islet cell sample 279


title: Pancreatic islet cell sample 281


title: Pancreatic islet cell sample 278


title: Pancreatic islet cell sample 280


title: Pancreatic islet cell sample 318


title: Pancreatic islet cell sample 277


title: Pancreatic islet cell sample 276


title: Pancreatic islet cell sample 275


title: Pancreatic islet cell sample 294


title: Pancreatic islet cell sample 271


title: Pancreatic islet cell sample 273


title: Pancreatic islet cell sample 269


title: Pancreatic islet cell sample 295


title: Pancreatic islet cell sample 272


title: Pancreatic islet cell sample 293


title: Pancreatic islet cell sample 267

value: Non T2D 2


title: Pancreatic islet cell sample 274


title: Pancreatic islet cell sample 270


title: Pancreatic islet cell sample 266


title: Pancreatic islet cell sample 261

value: Non T2D 1


title: Pancreatic islet cell sample 264

value: Pancreatic islets


title: Pancreatic islet cell sample 263


title: Pancreatic islet cell sample 260


title: Pancreatic islet cell sample 259


title: Pancreatic islet cell sample 265


title: Pancreatic islet cell sample 262


title: Pancreatic islet cell sample 257


title: Pancreatic islet cell sample 268


title: Pancreatic islet cell sample 253


title: Pancreatic islet cell sample 254


title: Pancreatic islet cell sample 255


title: Pancreatic islet cell sample 252


title: Pancreatic islet cell sample 256


title: Pancreatic islet cell sample 250


title: Pancreatic islet cell sample 248


title: Pancreatic islet cell sample 249


title: Pancreatic islet cell sample 247


title: Pancreatic islet cell sample 245


title: Pancreatic islet cell sample 246


title: Pancreatic islet cell sample 242


title: Pancreatic islet cell sample 243


title: Pancreatic islet cell sample 244


title: Pancreatic islet cell sample 240


title: Pancreatic islet cell sample 241


title: Pancreatic islet cell sample 258


title: Pancreatic islet cell sample 233


title: Pancreatic islet cell sample 234


title: Pancreatic islet cell sample 237


title: Pancreatic islet cell sample 230


title: Pancreatic islet cell sample 232


title: Pancreatic islet cell sample 231


title: Pancreatic islet cell sample 236


title: Pancreatic islet cell sample 229


title: Pancreatic islet cell sample 228


title: Pancreatic islet cell sample 227


title: Pancreatic islet cell sample 224


title: Pancreatic islet cell sample 251


title: Pancreatic islet cell sample 225


title: HP7-1WB_AV rep3

city: ShenZhen

first: Shangbo

last: Xie

address: BeiShanDao

country: China

institute: BGI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HP7-1 whole genome using BWA Version: 0.7.10-r789 with parameter: aln -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10
Clean reads mapped to HP7-1 whole gene datasets using Bowtie2 version 2.2.5 with parameter:-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Gene or Transcript expression was calculated by rsem-calculate-expression
Differrentially expressed gene screening was calculated by Possion Distribution method.And the samples group combined repeats was calculated by Noiseq package
Genome_build: HP7-1 whole genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Penicillium oxalicum

source_name: mycelium

growth_protocol: P. oxalicum strain HP7-1 (China General Microbiological Culture Collection (CGMCC) 10781) was isolated from a subtropical forest soil system in Guangxi Zhuang Autonomous Region, China [16], and its cellulase hyper-producing mutant,EU2106, (CGMCC 6471) was obtained by multiple 563 rounds of mutagenesis [17]. The strains were maintained on potato-dextrose-agar (PDA) plates at 4 ¡ãC. P. oxalicum strains were cultivated on PDA plates at 28 ¡ãC for 6 d to complete sporulation.

extract_protocol:
Total RNA was extracted from mycelia using the TRIzol? RNA Kit (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer¡¯s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: after 72 h of induction in the presence of wheat bran and Avicel

tag: genotype

value: wild type


title: Pancreatic islet cell sample 223

value: non-diabetic


title: Pancreatic islet cell sample 226

value: M


title: HP7-1WB_AV rep1


title: HP7-1WB_AV rep2


title: Pancreatic islet cell sample 222

value: alpha


title: Pancreatic islet cell sample 239


title: EU2106_WB_AV rep1

value: mutant type


title: Pancreatic islet cell sample 221


title: EU2106_WB_AV rep2


title: Pancreatic islet cell sample 238


title: Pancreatic islet cell sample 220


title: Pancreatic islet cell sample 235


title: EU2106_WB_AV rep3


title: Pancreatic islet cell sample 219


title: mRNA-Seq LPSDEX30min_Rep2

city: Tokorozawa

first: Hiroaki

last: Sako

country: Japan

institute: Waseda University

data_processing:
Base-calling and alignment were conducted by using the built-in Ion torrent software (V4.0.1). As reference sequences, the coding regions of each Ensemble gene (CDS + 25bp upstream of start site) were extracted using Biomart. When aligned to the reference gene sequences, sequenced reads shorter than 24bp were trimmed off.
For the processed files, raw read counts were converted to RPM (Reads Per Million) count.
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

organism: Mus musculus

growth_protocol: RAW 264 cells were cultured at 3.0 x 10^5 cells/ml in media (DMEM, 2mM Glutamine, 10% FBS, 100 units penicillin and 100µg streptomycin/mL) 24 hours prior to harvest.

extract_protocol:
Before extraction, cells were incubated with cycloheximide (final concentration of 100 µg/ml) and total RNA and then RPF and polyA mRNA were extracted by standard RiboSeq protocols.
RNA libraries were prepared for sequencing using standard Ion torrent protocols

treatment_protocol: Cells were stimulated by LPS (100 ng/ml for 30 min), or LPS+DEX (10uM) for 30 min before harvesting.

tag: cell line

value: RAW 264

tag: cell type

value: macrophages

tag: protocol

value: LPSDEX 30min

tag: profiling

value: mRNA-Seq


title: Ribo-Seq LPSDEX30min_Rep2

value: Ribo-seq


title: Ribo-Seq LPSDEX30min_Rep1


title: Pancreatic islet cell sample 218


title: Ribo-Seq Basal_Rep1

value: basal


title: Ribo-Seq LPS30min_Rep1

value: LPS 30min


title: mRNA-Seq LPSDEX30min_Rep1


title: Ribo-Seq Basal_Rep2


title: mRNA-Seq LPS30min_Rep2


title: Pancreatic islet cell sample 216

value: AA


title: mRNA-Seq LPS30min_Rep1


title: Pancreatic islet cell sample 214


title: Pancreatic islet cell sample 215


title: mRNA-Seq Basal_Rep1


title: Pancreatic islet cell sample 213


title: Pancreatic islet cell sample 211


title: mRNA-Seq Basal_Rep2


title: Pancreatic islet cell sample 209


title: Pancreatic islet cell sample 210


title: Ribo-Seq LPS30min_Rep2


title: Pancreatic islet cell sample 206

value: Non T2D 4

value: C

value: F

value: beta


title: Pancreatic islet cell sample 208

value: Pancreatic islets

value: Non T2D 1


title: Pancreatic islet cell sample 205

value: non-diabetic


title: Pancreatic islet cell sample 203


title: Pancreatic islet cell sample 202


title: Pancreatic islet cell sample 195

value: Non T2D 12

value: M


title: Pancreatic islet cell sample 198


title: Pancreatic islet cell sample 199


title: Pancreatic islet cell sample 197


title: Pancreatic islet cell sample 188


title: Pancreatic islet cell sample 194


title: Pancreatic islet cell sample 212

value: alpha


title: Pancreatic islet cell sample 192


title: Pancreatic islet cell sample 187


title: Pancreatic islet cell sample 200


title: Pancreatic islet cell sample 186


title: Pancreatic islet cell sample 189


title: Pancreatic islet cell sample 184


title: Pancreatic islet cell sample 193


title: Pancreatic islet cell sample 196


title: Pancreatic islet cell sample 182


title: Pancreatic islet cell sample 204


title: Pancreatic islet cell sample 181


title: Pancreatic islet cell sample 179


title: Pancreatic islet cell sample 180


title: Pancreatic islet cell sample 217


title: Pancreatic islet cell sample 178


title: Pancreatic islet cell sample 183


title: Pancreatic islet cell sample 177


title: Pancreatic islet cell sample 176


title: Pancreatic islet cell sample 207


title: Pancreatic islet cell sample 201


title: Pancreatic islet cell sample 191


title: Pancreatic islet cell sample 170


title: Pancreatic islet cell sample 174


title: Pancreatic islet cell sample 185


title: Pancreatic islet cell sample 171


title: Pancreatic islet cell sample 168


title: Pancreatic islet cell sample 173


title: Pancreatic islet cell sample 172


title: Pancreatic islet cell sample 163


title: Pancreatic islet cell sample 162


title: Pancreatic islet cell sample 167


title: Pancreatic islet cell sample 165


title: Pancreatic islet cell sample 161


title: Pancreatic islet cell sample 160


title: Pancreatic islet cell sample 158


title: Pancreatic islet cell sample 157


title: Pancreatic islet cell sample 159


title: Pancreatic islet cell sample 155


title: Pancreatic islet cell sample 156


title: Pancreatic islet cell sample 151


title: Pancreatic islet cell sample 150


title: Pancreatic islet cell sample 154


title: Pancreatic islet cell sample 153


title: Pancreatic islet cell sample 149


title: Pancreatic islet cell sample 175


title: Pancreatic islet cell sample 148


title: Pancreatic islet cell sample 147


title: Pancreatic islet cell sample 144

value: Non T2D 11

value: H


title: Pancreatic islet cell sample 145


title: Pancreatic islet cell sample 169


title: Pancreatic islet cell sample 190


title: Pancreatic islet cell sample 143


title: Pancreatic islet cell sample 164


title: Pancreatic islet cell sample 146


title: Pancreatic islet cell sample 138


title: Pancreatic islet cell sample 139


title: Pancreatic islet cell sample 140


title: Pancreatic islet cell sample 136


title: Pancreatic islet cell sample 135


title: Pancreatic islet cell sample 137


title: Pancreatic islet cell sample 166


title: Pancreatic islet cell sample 133

value: Non T2D 10


title: Pancreatic islet cell sample 134


title: Pancreatic islet cell sample 131


title: Pancreatic islet cell sample 132


title: Pancreatic islet cell sample 130


title: Pancreatic islet cell sample 129


title: Pancreatic islet cell sample 125


title: Pancreatic islet cell sample 128


title: Pancreatic islet cell sample 123


title: Pancreatic islet cell sample 122


title: Pancreatic islet cell sample 121


title: Pancreatic islet cell sample 126


title: Pancreatic islet cell sample 118


title: Pancreatic islet cell sample 119


title: Pancreatic islet cell sample 127


title: Pancreatic islet cell sample 142


title: Pancreatic islet cell sample 114


title: Pancreatic islet cell sample 115


title: Pancreatic islet cell sample 120


title: Pancreatic islet cell sample 112


title: Pancreatic islet cell sample 124


title: Pancreatic islet cell sample 108

value: Non T2D 9


title: Pancreatic islet cell sample 116


title: Pancreatic islet cell sample 117


title: Pancreatic islet cell sample 110


title: Pancreatic islet cell sample 113


title: Pancreatic islet cell sample 107


title: Pancreatic islet cell sample 106


title: Pancreatic islet cell sample 152


title: Pancreatic islet cell sample 104


title: Pancreatic islet cell sample 103


title: Pancreatic islet cell sample 101

value: Non T2D 8

value: AI


title: Pancreatic islet cell sample 109


title: Pancreatic islet cell sample 111


title: Pancreatic islet cell sample 96


title: Pancreatic islet cell sample 99


title: Pancreatic islet cell sample 98


title: Pancreatic islet cell sample 93

value: Non T2D 3


title: Pancreatic islet cell sample 95


title: Pancreatic islet cell sample 94


title: Pancreatic islet cell sample 97


title: Pancreatic islet cell sample 100


title: Pancreatic islet cell sample 92


title: Am_FW_input_rep1

city: Pune

first: Naveen

last: Prasad

state: Maharashtra

address: Dr Homi Bhaba Road

department: Biology

country: India

institute: IISER Pune

description: input DNA from fore wing of 1st biological replicate

library_source: genomic

data_processing:
The short reads were aligned to the genome of Apis mellifera verison 2.0 using bowtie.
Peaks were identified from the aligned files using MACS (version 1.4)
Genome_build: Amel2.0

molecule: genomic DNA

organism: Apis mellifera

source_name: fore wing buds from honey bee larvae

growth_protocol: wing buds were isolated from early fifth instar larvae of honey bee colonies. For details pl see Prasad N, Tarikere S, Khanale D, Habib F, Shashidhara LS. Evolution of insect hindwing morphology: A comparitive genomic analysis of targets of Hox protein Ultrabithorax (submitted)

extract_protocol:
pl see Prasad N, Tarikere S, Khanale D, Habib F, Shashidhara LS. Evolution of insect hindwing morphology: A comparitive genomic analysis of targets of Hox protein Ultrabithorax (submitted) for complete details.
libraries were prepared by using ChIP-seq DNA sample preparation kit (Illumina # IP- 102 -1001)

tag: developmental stage

value: early fifth larval instar

tag: tag

value: fore wing buds


title: Am_HW_input_rep2

description: input DNA from hind wing of2nd biological replicate

source_name: hind wing buds from honey bee larvae

value: hind wing buds


title: Pancreatic islet cell sample 91

value: C

value: F

value: beta


title: Am_FW_input_rep2

description: input DNA from fore wing of 2nd biological replicate


title: Am_HW_input_rep1

description: input DNA from hind wing of 2nd biological replicate


title: Am_HW_pre_immune_rep1

description: 1st biological replicate of pre immune ChIP (hind wing)


title: Pancreatic islet cell sample 89

value: Pancreatic islets

value: non-diabetic


title: Pancreatic islet cell sample 90


title: Am_HW_pre_immune_rep2

description: 2nd biological replicate of pre immune ChIP (hind wing)


title: Pancreatic islet cell sample 86


title: Pancreatic islet cell sample 105


title: Am_FW_pre_immune_rep2

description: 2nd biological replicate of pre immune ChIP (fore wing)


title: Am_FW_pre_immune_rep1

description: 1st biological replicate of pre immune ChIP (fore wing)


title: Pancreatic islet cell sample 87


title: Pancreatic islet cell sample 85

value: M


title: Pancreatic islet cell sample 102


title: Pancreatic islet cell sample 84


title: Am_HW_anti Ubx_rep2

description: 2nd biological replicate of anti Ubx ChIP (hind wing)


title: Pancreatic islet cell sample 83


title: Pancreatic islet cell sample 81


title: Am_HW_anti_Ubx_rep1

description: 1st biological replicate of anti Ubx ChIP (hind wing)


title: Am_FW_anti_Ubx_rep2

description: 2nd biological replicate of anti Ubx ChIP (fore wing)


title: Pancreatic islet cell sample 82


title: Pancreatic islet cell sample 78


title: Pancreatic islet cell sample 79


title: Pancreatic islet cell sample 72

value: Non T2D 7


title: Pancreatic islet cell sample 74


title: Pancreatic islet cell sample 80


title: Pancreatic islet cell sample 73


title: Pancreatic islet cell sample 76


title: Pancreatic islet cell sample 75


title: Pancreatic islet cell sample 77


title: Pancreatic islet cell sample 88


title: Pancreatic islet cell sample 69


title: Pancreatic islet cell sample 68


title: Pancreatic islet cell sample 66


title: Pancreatic islet cell sample 71


title: Pancreatic islet cell sample 64


title: Pancreatic islet cell sample 67


title: Pancreatic islet cell sample 65


title: Pancreatic islet cell sample 61


title: Pancreatic islet cell sample 63


title: Pancreatic islet cell sample 60


title: Am_FW_anti_Ubx_rep1

description: 1st biological replicate of anti Ubx ChIP (fore wing)


title: Pancreatic islet cell sample 62


title: Pancreatic islet cell sample 56

value: Non T2D 6


title: Pancreatic islet cell sample 55


title: Pancreatic islet cell sample 141

value: Non T2D 11

value: H


title: Pancreatic islet cell sample 53


title: Pancreatic islet cell sample 59


title: Pancreatic islet cell sample 54


title: Pancreatic islet cell sample 57


title: Pancreatic islet cell sample 58


title: ChIP-Seq analysis of HA-Phf5a in mouse ESCs under doxycycline treatment replicate 1

city: New York

first: Alexandros

last: Strikoudis

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the mouse genome (build mm10) using Bowtie1.
MACS1.4.2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction.
Genome_build: mm10
Supplementary_files_format_and_content: wig format containg genome-wide binding profile

source_name: ESC WITH LIF

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates.  ESC strain used: KH2 ESC line (C57BL/6 X 129/Sv) Original ESC reference: Beard C., et al. (2006). "Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells." Genesis 44(1): 23-28.

extract_protocol:
Ten million cells were used for the ChIP and precipitated using 5 micrograms of serum-purified antibodies. Original reference: Zhu B. et al. (2005) "The human PAF complex coordinates transcription with events downstream of RNA synthesis"
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: ESCs cultured in the presence LIF were treated with inducible shControl or shPhf5a knockdown using doxycycline (2μg/mL) for 3 days

value: mouse embryonic stem cells

tag: chip antibody

value: HA-antibody (Abcam, ab9110)


title: Pancreatic islet cell sample 47

value: Non T2D 5

value: AA


title: ChIP-Seq analysis of HA-Phf5a in mouse ESCs under absence of doxycycline treatment replicate 1


title: ChIP-Seq analysis of Cdc73 in mouse ESCs under shPhf5a knockdown treatment replicate 2

source_name: ESC shPhf5a WITH LIF

value: Cdc73 antibody, serum purified


title: ChIP-Seq analysis of HA-Phf5a in mouse ESCs under doxycycline treatment replicate 2


title: Pancreatic islet cell sample 44


title: Pancreatic islet cell sample 48


title: Pancreatic islet cell sample 50


title: Pancreatic islet cell sample 49


title: Pancreatic islet cell sample 70


title: ChIP-Seq analysis of Cdc73 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: ChIP-Seq analysis of HA-Phf5a in mouse ESCs under absence of doxycycline treatment replicate 2


title: ChIP-Seq analysis of Leo1 in mouse ESCs under shPhf5a knockdown treatment replicate 2

value: Leo1 antibody, serum purified


title: Pancreatic islet cell sample 46


title: Pancreatic islet cell sample 45


title: Pancreatic islet cell sample 40


title: Pancreatic islet cell sample 51


title: Pancreatic islet cell sample 52


title: Pancreatic islet cell sample 39


title: Pancreatic islet cell sample 38


title: ChIP-Seq analysis of Cdc73 in mouse ESCs under shControl knockdown treatment replicate 1

source_name: ESC shControl WITH LIF


title: Pancreatic islet cell sample 37


title: Pancreatic islet cell sample 43


title: ChIP-Seq analysis of Leo1 in mouse ESCs under shControl knockdown treatment replicate 2


title: ChIP-Seq analysis of Cdc73 in mouse ESCs under shControl knockdown treatment replicate 2


title: ChIP-Seq analysis of Leo1 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: Pancreatic islet cell sample 36


title: Pancreatic islet cell sample 41


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 2

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the mouse genome (build mm10) using Bowtie1.
MACS2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction.
Genome_build: mm10
Supplementary_files_format_and_content: wig format containg genome-wide binding profile

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates.  ESC strain used: KH2 ESC line (C57BL/6 X 129/Sv) Original ESC reference: Beard, C., et al. (2006). "Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells." Genesis 44(1): 23-28.

extract_protocol:
Ten million cells were used for the ChIP and precipitated using 10 micrograms of antibody  against Ser-5-Phosphoryalted RNA polymerase II (Abcam, ab5131 ) and  against Ser-2-Phosphoryalted RNA polymerase II (Active Motif, clone 3E10)
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

value: Ser-2-Phosphorylated RNA polymerase II:Active Motif, clone 3E10


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 3


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: Pancreatic islet cell sample 42


title: Pancreatic islet cell sample 35


title: ChIP-Seq analysis of Leo1 in mouse myotubes under shPhf5a knockdown treatment

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the mouse genome (build mm9) using Bowtie1.
MACS1.4.2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction.
Genome_build: mm9
Supplementary_files_format_and_content: wig format containg genome-wide binding profile

source_name: Myotubes shPhf5a

growth_protocol: C2C12 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Differentiation was induced by growing cells to confluence and supplementing the medium with 2% horse serum. After 72 hours in differentiation medium, differentiated myotubes were separated from undifferentiated cells with diluted trypsin. Original reference: Vethantham, V., et al. (2012). "Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 trimethylation during myogenic differentiation." Mol Cell Biol. 32(6):1044-55.

extract_protocol:
Ten million cells were used for the ChIP and precipitated using 5 micrograms of respective antibodies. Original reference: Zhu B. et al. (2005) "The human PAF complex coordinates transcription with events downstream of RNA synthesis"
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: C2C12 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Differentiation was induced by growing cells to confluence and supplementing the medium with 2% horse serum. After 72 hours in differentiation medium, differentiated myotubes were separated from undifferentiated cells with diluted trypsin. Cells were treated with shControl or shPhf5a knockdown hairpins.

value: mouse myotubes


title: ChIP-Seq analysis of Leo1 in mouse myotubes under shControl knockdown treatment

source_name: Myotubes shControl


title: Pancreatic islet cell sample 34


title: Pancreatic islet cell sample 33


title: Shoot_Pi-_polyA+_Rep2

city: Beijing

first: Jiapei

last: Yuan

state: Beijing

address: Tsinghua Yuan

institute: Tsinghua University

description:
WLSPA2
PolyA+
Strand information: fr-unstranded

data_processing:
Remove reads contain N and adapter sequence
Remove reads mapped to rRNA
Map to Arabidopsis genome using Tophat2
Remove duplicated reads
Calculate FPKM using eXpress
Do the differential expression using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKMs

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: shoots of seedlings, Col-0 P-

growth_protocol: The Pi sufficient medium (P+) contained half-strength MS salts with 1% (w/v) sucrose and 1.2% (w/v) agar (Sigma Cat. No. A1296). The formula of Pi deficient medium (P-) was the same as P+ medium except for replacing 1.25 mM KH2PO4 by 0.65 mM K2SO4. Seeds were surface sterilized with 20% (v/v) bleach for 15 min and washed in sterile-distilled water three times. After that, seeds were sown on Petri plates containing P+ or P- medium and stratified at 4°C for 2 days. The agar plates were placed vertically in a growth room at 22–24°C and with a photoperiod of 16 h of light and 8 h of darkness. The light intensity was 100 μmol m-2 s-1.

extract_protocol:
The total RNAs were extracted with the Trizol reagent (Invitrogen). After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN).
dUTP based strand-specific library construction protocol

treatment_protocol: Phosphate starvation

value: seedling

value: shoot

value: 10 days old

tag: ecotype

tag: genotype/variation

value: WT

tag: treatment

value: Phosphate deficiency


title: Shoot_Pi+_polyA-_Rep2

description:
WPSNA2
PolyA-
Strand information: fr-unstranded

source_name: shoots of seedlings, Col-0 P+

tag: tissue

value: Phosphate sufficiency


title: ChIP-Seq analysis of Leo1 in mouse myoblasts under shControl knockdown treatment

source_name: Myoblasts shControl

value: mouse myoblasts


title: Shoot_Pi-_polyA-_Rep2

description:
WLSNA2
PolyA-
Strand information: fr-unstranded

tag: age


title: ChIP-Seq analysis of Leo1 in mouse ESCs under shControl knockdown treatment replicate 1


title: Pancreatic islet cell sample 31

value: Pancreatic islets

tag: donor id

tag: condition

value: non-diabetic

tag: ethnicity

value: M

value: beta


title: Root_Pi-_polyA-_Rep2

description:
WLRNA2
PolyA-
Strand information: fr-firststrand

source_name: roots of seedlings, Col-0 P-

value: root


title: Sequencing analysis of input in mouse myotubes under shControl knockdown treatment

value: Input


title: Sequencing analysis of input in mouse myoblasts under shControl knockdown treatment


title: Pancreatic islet cell sample 29

value: Non T2D 5

value: AA

tag: gender

tag: cell subtype


title: RNA-Seq analysis in mouse ESCs after shPaf1 knockdown replicate 3

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were aligned to the mm9 genome assembly using Tophat
Gene expression analysis was performed for each matched samples, separately in each biological replicate. Two types of comparisons were tested: (a) shControl vs shPhf5a knockdown and (b) shControl vs shPaf1 knockdown, Analysis was performed using Cufflinks.
Two types of comparisons were tested: (a) shControl vs shPhf5a knockdown and (b) shControl vs shPaf1 knockdown, Analysis was performed using Cufflinks.
Genome_build: mm9

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates. ESC strain used: KH2 ESC line (C57BL/6 X 129/Sv) Original ESC reference: Beard, C., et al. (2006). "Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells." Genesis 44(1): 23-28.

extract_protocol:
Trizol reagent extraction (Invitrogen)
cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: ESCs cultured in the presence of LIF, and treated with inducible shControl, shPhf5a or shPaf1 knockdown using doxycycline (2μg/mL)

value: mouse embryonic stem cells


title: Pancreatic islet cell sample 30


title: Root_Pi-_polyA+_Rep2

description:
WLRPA2
PolyA+
Strand information: fr-firststrand


title: Root_Pi+_polyA-_Rep2

description:
WPRNA2
PolyA-
Strand information: fr-firststrand

source_name: roots of seedlings, Col-0 P+


title: Pancreatic islet cell sample 28

value: Non T2D 3

value: C

value: F


title: RNA-Seq analysis in mouse ESCs after shPaf1 knockdown replicate 2


title: Pancreatic islet cell sample 27


title: Root_Pi+_polyA+_Rep2

description:
WPRPA2
PolyA+
Strand information: fr-firststrand

value: seedling

value: 10 days old


title: RNA-Seq analysis in mouse ESCs after shPhf5a knockdown replicate 3


title: Pancreatic islet cell sample 26

value: Non T2D 2


title: RNA-Seq analysis in mouse ESCs after shPaf1 knockdown replicate 1


title: Pancreatic islet cell sample 25


title: Shoot_Pi-_polyA-_Rep1

description:
WLSNA1
PolyA-
Strand information: fr-firststrand

value: shoot

value: WT

value: Phosphate deficiency


title: RNA-Seq analysis in mouse ESCs after shPhf5a knockdown replicate 2


title: Pancreatic islet cell sample 32

value: Pancreatic islets

value: non-diabetic


title: Shoot_Pi-_polyA+_Rep1

description:
WLSPA1
PolyA+
Strand information: fr-firststrand


title: Shoot_Pi+_polyA-_Rep1

description:
WPSNA1
PolyA-
Strand information: fr-firststrand

value: Phosphate sufficiency


title: Pancreatic islet cell sample 24

value: beta


title: Shoot_Pi+_polyA+_Rep2

description:
WPSPA2
PolyA+
Strand information: fr-unstranded


title: Pancreatic islet cell sample 23


title: RNA-Seq analysis in mouse ESCs after shControl knockdown replicate 3


title: RNA-Seq analysis in mouse ESCs after shPhf5a knockdown replicate 1


title: RNA-Seq analysis in mouse ESCs after shControl knockdown replicate 2


title: Pancreatic islet cell sample 21


title: RNA-Seq analysis in mouse ESCs after shControl knockdown replicate 1


title: Lane B-Snf2h cKO-Nestin Runner

city: Ottawa

first: Matias

last: Alvarez-Saavedra

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
Pool of 3 independent cerebella
processed data file: KOR vs WTR.xls

data_processing:
base calling: TopHat software version 2.0.8b (http://ccb.jhu.edu/software/tophat/index.shtml) was used for processing reads.
Transcript Assembly: Cufflinks software (v2.1.1).
Transcriptome Assembly: Cuffmerge (v1.0.0).
Differenatial Expression: Cuffdiff and CummeRbund.
Genome_build: UCSC mouse genome (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for the samples.

source_name: Cerebellum

growth_protocol: Control and Snf2h cKO-Nestin mice in sedentary or running conditions.

extract_protocol:
Trizol (Invitrogen) + RNA-clean up column (Qiagen)
2 x 100 bases per lane, paired-end, HiSeq 2000

treatment_protocol: Cerebella quickly dissected and snap frozen in dry ice.

tag: activity status

value: runner

tag: strain

value: Cerebellum

tag: genotype

value: Snf2h cKO

value: Postnatal day 40

tag: Sex

value: Male


title: H3K4Me3 in wt

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
H3K4me3 data : Illumina pipeline V1.3 was used for image analysis and basecalling. Sequence reads were mapped to reference genome mm9/NCBI37 using Eland (eland_extended).
Illumina Casava1.8 software was used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Please note that bed files were used to generate heat maps with ChIP-seq data interpretation platform seqMINER (seqMINER: an integrated ChIP-seq data interpretation platform. Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L. Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.). No other (further) processed data as seqMINER illustrates well enough our conclusions.
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: testis wt

extract_protocol:
ChIPed DNA was purified by phenol/chloroform extraction
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881,Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 7pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

tag: strain  background

value: wild type

value: testis

value: H3K4Me3 (04-745, Millipore)


title: H3K4Me3 in TRF2-/-

source_name: testis TRF2 -/-


title: PolII in TRF2-/-

value: PolII (sc-9001X, Santa Cruz)


title: Pancreatic islet cell sample 19

source_name: Pancreatic islets

value: Non T2D 2

value: C

value: F


title: Pancreatic islet cell sample 18


title: PolII in TRF2tag/tag

source_name: testis TRF2 tag/tag

value: TRF2 tag/tag


title: Lane B-Control Runner

description:
Pool of 3 independent cerebella
processed data file: WTR vs WTS.xls

value: control


title: TBP in TRF2-/-

value: TBP (ab28175, Abcam), TBP (ab51841, Abcam)


title: Lane B-Snf2h cKO-Nestin Sedentary

description:
Pool of 3 independent cerebella
processed data file: KOS vs KOR.xls

value: sedentary


title: Pancreatic islet cell sample 17

value: Pancreatic islets

value: non-diabetic

value: beta


title: TRF2 in TRF2-/-

value: Flag (M2 affinity gel, Sigma), TRF2 (in house)


title: Lane A-Snf2h cKO-Nestin Runner

value: runner

value: Cerebellum

value: Snf2h cKO

value: Postnatal day 40


title: Pancreatic islet cell sample 22


title: Lane B-Control Sedentary

description:
Pool of 3 independent cerebella
processed data file: WTS vs KOS.xls

value: Male


title: Shoot_Pi+_polyA+_Rep1

description:
WPSPA1
PolyA+
Strand information: fr-firststrand

tag: developmental stage

value: seedling

value: shoot

value: 10 days old

value: WT

value: Phosphate sufficiency


title: TRF2 in TRF2 tag/tag

value: TRF2 tag/tag

value: testis

tag: chip antibody


title: Pancreatic islet cell sample 15

value: Non T2D 2

value: C

value: F


title: Pancreatic islet cell sample 14

value: Pancreatic islets

value: non-diabetic

value: beta


title: Lane A-Control Runner

value: runner

value: Cerebellum

value: control


title: KO_rep3

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Reads were mapped onto the mm9 assembly of the Mus musculus genome by using Tophat 2.0.10 and bowtie-2-2.1.0.
Quantification of gene expression has been performed using HTSeq-0.5.4p3.
Normalization was performed using DESeq2 1.0.19.
Genome_build: mm9
Supplementary_files_format_and_content: raw_and_normalize count

extract_protocol:
Total RNA was extracted using Tri Reagent (Molecular Research Center, TR118)
Libraries of template molecules suitable for high throughput DNA sequencing were created using “TruSeq™ Stranded Total RNA LT library prep kit with Ribo-Zero Gold” (Illumina Inc.) according to manufacturer’s user guide (Rev E oct 2013). Briefly, 300 ng of total RNA were depleted in ribosomal RNA using biotinylated, target-specific oligos combined with Ribo-Zero™ removal beads. Following purification, RNA were fragmented using divalent cations at 94°C for 8 minutes. The cleaved RNA fragments were then reverse transcribed to cDNA using random primers and the second strand of cDNA was synthesized using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters were generated in the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

value: post natal day 21


title: KO_rep2


title: Lane A-Snf2h cKO-Nestin Sedentary

value: sedentary

value: Snf2h cKO

value: Postnatal day 40

value: Male


title: Lane A-Control Sedentary


title: KO_rep1


title: WT_rep3

source_name: wild type_testis

value: wild type


title: Pancreatic islet cell sample 11

value: Non T2D 1

value: AA

value: M


title: WT_rep2

value: testis


title: Pancreatic islet cell sample 12


title: Pancreatic islet cell sample 16

value: Non T2D 2

value: C

value: F


title: Dnm3a-mutant PTCL Sample 2 (RRBS)

city: Omaha

first: Rene

last: Opavsky

state: NE

address: 985040 Nebraska Medical Center

institute: University of Nebraska Medical Center

description: RRBS

data_processing:
For RNAseq data sequences were aligned using TopHat2 aligner and Cufflinks was used to generate FPKM values and perform statistical analysis.
Whole genome bisulfite sequencing (WGBS): Linker sequences were removed using fqtrim (version 0.94). Sequence tags were aligned with the mouse genome (Dec. 2011 Mus musculus assembly mm10, Build 38) and individual CpG sequencing coverage and methylation levels were determined using the methyl-seq software Bismark (version 0.14.3) running the sequence aligner bowtie2 (version 2.2.3) using standard software settings.
Reduced Representation Bisulfite Sequencing (RRBS): The Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS, version 1.0) was used to trim, align and determine the methylation status of CpGs associated with this type of restriction digest high throughput method using standard software settings. Sequences were initially aligned with genome mm9 then converted to mm10 using the UCSC Genome Browser Batch Coordinate Conversion (liftOver) utility.
Genome_build: mm10
Supplementary_files_format_and_content: [RNA-seq]  .txt files report FPKMs.
Supplementary_files_format_and_content: [WGBS] Tab delimited .txt file. Columns = CpG chromosome, CpG chromosome base location (mm10), CpG chromosome base location (mm10), percent methylation, methylated sequence counts and unmethylated sequence counts.
Supplementary_files_format_and_content: [RRBS] Tab delimited .txt file. Columns = CpG chromosome, CpG chromosome base location (mm10), strand, methylated sequence counts, unmethylated sequence counts, and percent methylation.

source_name: spleen

extract_protocol:
gDNA and RNA were isolated from splenic FACS sorted splenic B-1a and CD8+ cells using standard methods.
Library generation for WGBS, RRBS, and RNAseq were performed using standard methods

tag: background strain

value: N/FVB

tag: sample type

value: tumor PTCL


title: Pancreatic islet cell sample 8

value: Pancreatic islets

value: non-diabetic

value: beta


title: WT_rep1

tag: genotype/variation

value: post natal day 21


title: Pancreatic islet cell sample 7

tag: tissue


title: Pancreatic islet cell sample 6

tag: age


title: Dnm3a-mutant PTCL Sample 1 (RRBS)

description: RRBS


title: TissueFC

city: BOSTON

first: Jesse

last: Gray

state: Massachusetts

address: 77 AVENUE LOUIS PASTEUR, NRB room 0356

department: Genetics

institute: Harvard Medical School

data_processing:
align using RUM to mm9
map to features using custom script
call differential gene expression using edgeR
Genome_build: mm9 using RUM version 1.11
Supplementary_files_format_and_content: read counts, counts per million

source_name: cortical neurons

extract_protocol:
Manual cell sorting and RNA sequencing. Manual sorting of fluorescent cells was carried out as first described in24. Briefly, Arc-dVenus transgenic male C57BL/6 mice were sacrificed under isoflurane anesthesia 6hrs after behavioral procedures and their brains were quickly removed and transferred into ice-cold oxygenated ACSF, containing 126 mM NaCl, 20 mM NaHCO3, 20 mM dextrose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM MgCl2, 50 mM APV, 20 mM DNQX, 100 nM TTX. Acute 330 μm coronal brain slices were prepared and incubated in a protease E (1.2 mg/mL) (Sigma) containing oxygenated ACSF for 50min. After 15min of washes in the ACSF, TeA tissue was microdissected using a pair of fine scissors under a fluorescent dissecting microscope (Leica M165FC). The dissected TeA tissue was then triturated in ACSF using a series of three Pasteur pipettes of decreasing tip diameters, and the dissociated cells were transferred into a small petri dish. With visual control under a fluorescent dissecting microscope, Venus+ neurons were aspirated into a micropipette with a 30–50 μm tip diameter and transferred into a clean petri dish. A total of 35–60 Venus+ neurons were pooled for each sample, which were immediately lysed in 50 μl of extraction buffer (PicoPure RNA isolation kit, Arcturus, Life Technologies) and total mRNA was subsequently isolated. cDNA was synthesized using Ovation RNA-Seq System V2 kit (Nugen). We obtained approximately 6 μg of cDNA from 35–60 cells from each group.
the cDNA library was prepared using Ovation Ultralow DRMultiplex Systems (Nugen). Sequencing was conducted on an Illumina HiSeq2000.

treatment_protocol: For the RNA sequencing study, the Arc-dVenus transgenic mice were divided into three different groups. One group (FC, n = 3) went through the FC and received 7 CS (10 sec, 6khz pure tone) and US pairing (1 sec, 0.5mA). Another group (Shock, n = 2) received 7 repetitions of US (1-s footshock, 0.5mA DC; inter-trial interval: 20-180s) without any CSs. The bulk-tissue controls included one mouse that was put into the conditioning chamber and did not receive any CS nor US, two mice that were shocked without tones, and one mouse that was fear conditioned. All Arc-dVenus transgenic mice were sacrificed 6hrs after the behavioral procedures.

value: Post natal day 60-90

tag: treatment

value: Fear conditioned

value: cortex

value: Arc-dVenus +/-


title: FC23

value: fear conditioned


title: Shock33

value: Shock only


title: TissueShock2


title: Sequencing analysis of input in mouse myotubes under shPhf5a knockdown treatment

tag: cell type

value: mouse myotubes

value: Input


title: FC40


title: TBP in TRF2tag/tag

value: TRF2 tag/tag

value: testis

value: TBP (ab28175, Abcam), TBP (ab51841, Abcam)


title: WT CD8+ T-cell Sample 1 (RRBS)

description: RRBS

value: N/FVB

value: normal CD8 cells

value: WT


title: Pancreatic islet cell sample 5

value: Pancreatic islets

tag: donor id

value: Non T2D 1

tag: condition

value: non-diabetic

tag: ethnicity

value: AA

value: M


title: Pancreatic islet cell sample 10

tag: gender

tag: cell subtype

value: beta


title: Pancreatic islet cell sample 13


title: FC39

tag: strain

value: Post natal day 60-90

value: cortex

tag: genotype

value: Arc-dVenus +/-


title: Pancreatic islet cell sample 3


title: Dnm3a-mutant PTCL Sample 3 (RNA-seq)

description: processed data file: CD8_vs_PTCL_CuffDiff.txt.gz

value: tumor PTCL


title: Pancreatic islet cell sample 4


title: Pancreatic islet cell sample 9


title: Dnm3a-mutant PTCL Sample 1 (RNA-seq)


title: Pancreatic islet cell sample 2


title: Dnm3a-mutant CLL sample 2 (RRBS)

description: RRBS

value: tumor mutant CLL


title: Shock30

value: Shock only


title: WT B1 sample 1 (RRBS)

description: RRBS

value: normal B1 cells


title: Pancreatic islet cell sample 1


title: WT B1 sample 2 (RRBS)

description: RRBS


title: UT-SCC118 PICSAR siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: RNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq2500 instrument using single-end sequencing with 50bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software and aligned against the human reference genome (GRCh37 assembly, downloaded from UCSC) using TopHat version 2.0.6.
After alignment, the reads were associated with known genes based on RefSeq annotations derived from UCSC and the number of reads aligned within each gene was counted using HTSeq tool (v.0.5.4p3).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12).
Genome_build: GRCh37
Supplementary_files_format_and_content: For statistical testing the data were further log transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values.

source_name: Cutaneous squamous cell carcinoma 118

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starvated 24 hours before harvesting.

tag: source

value: Cutaneous squamous cell carcinoma

value: Derived from cSCC tumors

value: Primary cSCC cells

value: PICSAR siRNA


title: WT CD8+ T-cell Sample 2 (RRBS)

description: RRBS

value: N/FVB

value: normal CD8 cells

value: WT


title: WT CD8+ T-cell Sample 2 (RNA-seq)


title: UT-SCC59A PICSAR siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 59A


title: Dnm3a-mutant CLL sample 8 (RNA-seq)

description: processed data file: B1_vs_MutCLL_CuffDiff.txt.gz


title: Dnm3a-mutant CLL sample 7 (RNA-seq)


title: Dnm3a-mutant CLL sample 4 (RNA-seq)


title: Dnm3a-mutant PTCL Sample 2 (RNA-seq)


title: UT-SCC118 negative control siRNA

description: RNA sequencing data from cSCC

value: Negative control siRNA


title: Dnm3a-mutant CLL sample 6 (RNA-seq)


title: Dnmt3a-Heterozygous CLL sample 3 (RNA-seq)

description: processed data file: B1_vs_HetCLL_CuffDiff.txt.gz

value: tumor Het CLL


title: Dnm3a-mutant CLL sample 5 (RNA-seq)


title: Pancreatic islet cell sample 20

value: Pancreatic islets

value: Non T2D 2

value: non-diabetic

value: C

value: F

value: beta


title: UT-SCC59A negative control siRNA

description: RNA sequencing data from cSCC


title: Dnm3a-mutant CLL sample 1 (RRBS)

description: RRBS

value: tumor mutant CLL


title: WT B1 sample 2 (RNA-seq)

description:
processed data file: B1_vs_HetCLL_CuffDiff.txt.gz
processed data file: B1_vs_MutCLL_CuffDiff.txt.gz

value: normal B1 cells


title: Dnmt3a-Heterozygous CLL sample 2 (RNA-seq)


title: Dnm3a-mutant CLL sample 3 (RNA-seq)


title: MYOCD-1

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

description: Control Empty virus transduced

data_processing:
In this analysis, two iterations of TopHat alignment were performed in order to maximize the chance of identification of exon-exon junctions. The aligned data for each sample were used independently by two complementary programs, Scripture and Cufflinks, for assembling transcripts independent of gene annotation.  We determined the threshold for the read coverage of each transcript across all samples by optimizing the sensitivity and specificity for identifying full length versus partial length transcripts of protein coding genes in RefSeq.  In the end, we kept assembled transcripts present in both Scripture and Cufflinks outputs, and with ≥2 exons, ≥200 bp and ≥ 2.7 read coverage as reads below this threshold were deemed unreliable in predicting exon structure.  Next, we eliminated all transcripts that had an exon overlapping in the same strand with known transcripts from available databases.  We then computed the coding potential of all remaining putative novel transcripts using PhyloCSF (53) and removed any transcripts containing an open reading frame with PhyloCSF score ≥ 100 across all three reading frames.  We further removed transcripts that were homologous to known protein coding domains in the Pfam database (release 26; both PfamA and PfamB) using the program HMMER-3 (e-value = 10).  Lastly, we computed expression values (in FPKM, fragments per kilobase of exon per million fragments mapped) of those defined nlncRNAs in the bed file.  The final list of lncRNAs comprises transcripts with FPKM >1
Genome_build: hg19
Supplementary_files_format_and_content: BED file; exonic structure of novel long non-coding RNAs: 1. chromosome: chromosome of defined nlncRNA  2. transcript_start: the starting position of the nlncRNA n the chromosome  3. transcript_end:the ending position of the nlncRNA n the chromosome  4. transcript_ID: temporary IDs of the nlncRNA    5. score_(meaningless): no specific meaning.      6. strand: strand of the nlncRNA  7. transcript_start: same as 2  8. transcript_end: same as 3    9. RGB(meaningless): no specific meaning.           10. number of exon:how many exons of the nlncRNAs  11. A comma-separated list of the exon sizes          12. A comma-separated list of the exon starting position relative to transcript start position
Supplementary_files_format_and_content: MYOCD_FPKM.xlsx; FPKM  value of those defined nlncRNAs in the bed file

source_name: vascular smooth muscle cell (HCASMs)

growth_protocol: HCASMs grow in 231 medium supplemented with growth supplement (SMG)

extract_protocol:
RNA was extracted by miReasy from Qiagen
mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size.

treatment_protocol: We transduced the adenovirus in growing HCASMs for 3 days and total RNA was extracted for RNA-seq.

tag: transduction

value: ad-MYOCD


title: UT-SCC12A negative control siRNA

description: RNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 12A

value: Cutaneous squamous cell carcinoma

value: Derived from cSCC tumors


title: Dnm3a-mutant PTCL (WGBS)

description: WGBS

value: tumor PTCL


title: UT-SCC12A PICSAR siRNA

description: RNA sequencing data from cSCC

value: Primary cSCC cells

value: PICSAR siRNA


title: Dnm3a-mutant CLL sample 2 (RNA-seq)

value: N/FVB


title: WT CD8+ T-cell Sample 1 (RNA-seq)

value: normal CD8 cells

value: WT


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shPhf5a knockdown treatment replicate 2

data_processing:
Basecalls performed using Illumina bcl2fastq.
ChIP-seq reads were aligned to the mouse genome (build mm10) using Bowtie1.
MACS1.4.2 was used for peak discovery. GenomicTools was used for ChIP-seq profile construction. Input samples for this study accessioned as GSM1894005 and GSM1894006 in GSE73444.
Genome_build: mm10
Supplementary_files_format_and_content: wig format containg genome-wide binding profile

source_name: ESC shPhf5a WITH LIF

extract_protocol:
Ten million cells were used for the ChIP and precipitated using 2 micrograms of serum-purified antibody against Paf1. Original reference: Zhu B. et al. (2005) "The human PAF complex coordinates transcription with events downstream of RNA synthesis"
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

value: mouse embryonic stem cells

tag: cell line

tag: chip antibody

value: Paf1 antibody, serum purified


title: Dnm3a-mutant CLL sample 1 (RNA-seq)

tag: background strain

tag: sample type


title: MYOCD-2

description: Control Empty virus transduced


title: Dnmt3a-Heterozygous CLL sample 4 (RNA-seq)

value: tumor Het CLL

tag: genotype/variation


title: Ctrl2

description: MYOCD overexpression

value: empty control


title: Dnmt3a-Heterozygous CLL sample 1 (RNA-seq)


title: Dnm3a-mutant CLL (WGBS)

description: WGBS


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shControl knockdown treatment replicate 3

source_name: ESC shControl WITH LIF


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shPhf5a knockdown treatment replicate 3


title: WT CD8+ T-cell (WGBS)

description: WGBS


title: Ctrl1

description: MYOCD overexpression


title: Dnmt3a-Heterozygous CLL  (WGBS)

description: WGBS


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shControl knockdown treatment replicate 2


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: WT B1 sample 1 (RNA-seq)


title: WT B1  (WGBS)

description: WGBS


title: ChIP-Seq analysis of Paf1 in mouse ESCs under shControl knockdown treatment replicate 1


title: TissueShock1

tag: age

value: Post natal day 60-90

value: Shock only

tag: tissue

value: cortex

value: Arc-dVenus +/-


title: Sequencing analysis of input in mouse ESCs under shPhf5a knockdown treatment for PolII and Paf1 ChIP

tag: cell type

value: none (input)


title: villous_S13

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

data_processing:
Libraries were sequenced on the Illumina Hi-Seq 2500. Basecalls were performed with CASAVA version 1.8.
Sequence adapters were trimmed using AdapterRemoval with options --trimns, --minlength 20. Trimmed RNA-Seq reads were aligned to known UCSC hg19 genes and the hg19 genome using Bowtie 2 v2.1.0 and TopHat v2.0.9 with options --library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180. UCSC hg19 reference genome and transcriptome was obtained through Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html).
Aligned RNA-Seq reads were summarised using the summarizeOverlaps algorithm with the UCSC known genes hg19 GTF file using the the options overlapMode=``Union'', ignoreStrand=FALSE, singleEnd=FALSE, fragments=TRUE to generate a table of unique read counts per gene for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: A count table of uniquely mapped read pairs overlapping genes.

source_name: placental villous tissue

extract_protocol:
RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with mix 1 or mix 2 of the 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts.
Ribosomal RNAs were depleted from samples using Ribo-Zero Gold.  and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol at the Australian Cancer Genomics Facility in Adelaide.

treatment_protocol: Placenta samples were collected and dissected post-delivery and incubated in RNAlater solution at 4 degrees celcius for 24 hours before being stored at -80 degrees celcius.

tag: ercc spike-in pool

tag: fetal sex

value: Male

tag: gestational age (weeks)

value: placental villous tissue


title: villous_S14

value: Female


title: villous_S16


title: villous_S12


title: Lark 3rd Instar Wing Disc Replicate 1

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

description: Lark.wing.ave.log.enrichment.sgr

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using default settings
Aligmentment to the Drosophila release 5 genome sequence was performed using the TMAP map4 algorithm without soft clipping (-g 3 option)
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDtools genomecoveragebed (-d option)
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using R scripts as described elsewhere (Dorsett and Misulovin. 2016. Meth Mol Biol, in press). Coverage in each window was normalized to total genome coverage prior to normalization to Input.
ChIP enrichment was averaged for all replicates to generate final processed data files
Genome_build: Drosophila melanogaster Release 5 (April 2006) with ChrU and Uextra removed
Supplementary_files_format_and_content: Text graph file (sgr) of log2 enrichment normalized to Input

organism: Drosophila melanogaster

source_name: y w male 3rd instar wing discs

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol:
BG3 cells were grown to a concentration of 5E6 per mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x109/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x106 cells, were snap frozen on dry ice. For immunoprecipitation, aliquots of chromatin (10 - 20 x 106 BG3 cells) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns or phenol/choloroform extraction and ethanol precipitation.
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Plus Fragment Library Kit (Life Technologies) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: antibody

value: Lark

tag: protocol

value: no treatment


title: Sequencing analysis of input in mouse ESCs under shControl knockdown treatment for PolII and Paf1 ChIP

tag: strain


title: villous_S11


title: TBPH 3rd Instar Wing Disc Replicate 2

description: TBPH.wing.ave.log.enrichment.sgr

value: TBPH


title: TBPH 3rd Instar Wing Disc Replicate 1

description: TBPH.wing.ave.log.enrichment.sgr


title: villous_S15


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 3

value: Ser-2-Phosphorylated RNA polymerase II:Active Motif, clone 3E10


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 2


title: villous_S10


title: villous_S9


title: ChIP-Seq analysis of Ser2-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 1


title: Nipped-B 3rd Instar Wing Disc Replicate 2

description: NipB.wing.ave.log.enrichment.sgr

value: Nipped-B


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 3

value: mouse embryonic stem cells

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5136


title: Lark 3rd Instar Wing Disc Replicate 2

description: Lark.wing.ave.log.enrichment.sgr


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 2

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5135


title: villous_S7


title: villous_S6


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shPhf5a knockdown treatment replicate 1

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5134


title: Lark triptolide 4 hour Technical Replicate 2

description: Lark.BG3.trp.10uM.4hr.ave.log.enrichment.sgr

source_name: ML-DmBG3-c2 cultured cells

value: 10 micromolar triptolide treatment


title: Lark triptolide 4 hour Technical Replicate 1


title: villous_S8


title: villous_S5


title: villous_S4


title: Lark triptolide 2 hour Technical Replicate 1

description: Lark.BG3.trp.10uM.2hr.ave.log.enrichment.sgr


title: Lark triptolide 1 hour Technical Replicate 2

description: Lark.BG3.trp.10uM.1hr.ave.log.enrichment.sgr


title: Lark triptolide 2 hour Technical Replicate 2


title: villous_S3


title: Nipped-B 3rd Instar Wing Disc Replicate 1

description: NipB.wing.ave.log.enrichment.sgr


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 3

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5133


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 1

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5131


title: Lark triptolide 1 hour Technical Replicate 1


title: villous_S2


title: villous_S1


title: ChIP-Seq analysis of Ser5-Phosphorylated_PolII in mouse ESCs under shControl knockdown treatment replicate 2

value: Ser-5-Phosphorylated RNA polymerase II:Abcam, ab5132


title: TBPH triptolide 4 hour

description: TBPH.BG3.trp.10uM.4hr.log.enrichment.sgr


title: Sequencing analysis of input in mouse ESCs under shPhf5a knockdown treatment for replicate 2 and 3

description: ESC-shPhf5a-Input-H3K79me2-shPhf5a-rep2-and-3

extract_protocol:
Ten million cells were treated withmicrococcal nuclease to generate mono-nucleosomes and for the ChIP chromatin was precipitated using 10 micrograms of antibody against H3K4me3 (Millipore, 07-473), H3K79me2 (Active Motif, 39143) and H3K36me3 (Abcam, ab9050).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

value: Input (none)


title: Sequencing analysis of input in mouse ESCs under shPhf5a knockdown treatment


title: Sequencing analysis of input in mouse ESCs under shControl knockdown treatment

description: ESC-shControl-Input


title: Nipped-B triptolide 2 hour

description: NipB.BG3.trp.10uM.2hr.log.enrichment.sgr


title: Nipped-B triptolide 1 hour

description: NipB.BG3.trp.10uM.1hr.log.enrichment.sgr


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shControl knockdown treatment replicate 3

value: H3K36me3 (Abcam, ab9050)


title: TBPH triptolide 1 hour

description: TBPH.BG3.trp.10uM.1hr.log.enrichment.sgr


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shPhf5a knockdown treatment replicate 3


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shControl knockdown treatment replicate 1


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shPhf5a knockdown treatment replicate 2


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: Ser5P triptolide 4 hour

description: Ser5P.PolII.BG3.trp.10uM.4hr.log.enrichment.sgr


title: Ser5P triptolide 2 hour

description: Ser5P.PolII.BG3.trp.10uM.2hr.log.enrichment.sgr


title: Nipped-B triptolide 4 hour

description: NipB.BG3.trp.10uM.4hr.log.enrichment.sgr


title: Ser5P triptolide 1 hour

description: Ser5P.PolII.BG3.trp.10uM.1hr.log.enrichment.sgr


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shPhf5a knockdown treatment replicate 3

value: H3K79me2 (Active Motif, 39143)


title: Lark Nipped-B RNAi Replicate 2

value: Nipped-B RNAi treatment


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shPhf5a knockdown treatment replicate 2


title: TBPH triptolide 2 hour

description: TBPH.BG3.trp.10uM.2hr.log.enrichment.sgr


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shControl knockdown treatment replicate 3


title: TBPH Nipped-B RNAi Replicate 3


title: TBPH Nipped-B RNAi Replicate 2


title: TBPH Nipped-B RNAi Replicate 4


title: Root_Pi-_polyA+_Rep1

description:
WLRPA1
PolyA+
Strand information: fr-unstranded

source_name: roots of seedlings, Col-0 P-

tag: developmental stage

value: seedling

value: root

value: 10 days old

tag: ecotype

value: WT

tag: treatment

value: Phosphate deficiency


title: Root_Pi-_polyA-_Rep1

description:
WLRNA1
PolyA-
Strand information: fr-unstranded


title: ChIP-Seq analysis of H3K36me3 in mouse ESCs under shControl knockdown treatment replicate 2

value: mouse embryonic stem cells

tag: cell line


title: Root_Pi+_polyA-_Rep1

description:
WPRNA1
PolyA-
Strand information: fr-unstranded

source_name: roots of seedlings, Col-0 P+

value: Phosphate sufficiency


title: Root_Pi+_polyA+_Rep1

description:
WPRPA1
PolyA+
Strand information: fr-unstranded


title: TBPH Nipped-B RNAi Replicate 1

value: TBPH


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shPhf5a knockdown treatment replicate 3

tag: chip antibody

value: H3K4me3 (Millipore, 07-473)


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shControl knockdown treatment replicate 1


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shPhf5a knockdown treatment replicate 1


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shControl knockdown treatment replicate 2


title: Nipped-B Lark RNAi Replicate 1

value: Nipped-B

value: Lark RNAi treatment


title: SA Lark RNAi Replicate 1

value: SA


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shControl knockdown treatment replicate 3


title: Nipped-B Lark RNAi Replicate 2


title: SA TBPH RNAi Replicate 2

value: TBPH RNAi treatment


title: Lark Nipped-B RNAi Replicate 1

value: Lark


title: SA TBPH RNAi Replicate 1


title: GRO-Seq analysis in mouse ESCs under shPaf1 knockdown treatment for 3 days replicate 3

description:
processed_data_file: GRO-SEQ-mESC-shPaf1-DOX_3days.minus.bw
processed_data_file:  GRO-SEQ-mESC-shPaf1-DOX_3days.plus.bw

data_processing:
Library strategy: GRO-seq
Basecalls performed using CASAVA
RNA-seq reads were aligned to the mm9 genome assembly using Tophat
Pausing index analysis was performed for each matched samples, separately in each biological replicate and treatment. Two types of comparisons were tested: (a) shControl vs shPhf5a knockdown for 3 days each and (b) Comparison of shControl, shPhf5a, shPaf1 ESCs, differentiated ESCs and flavopiridol-treated ESCs, respectively. Analysis was performed using the DEGseq25 package.
Two types of comparisons were tested: (a) shControl vs shPhf5a knockdown for 3 days each and (b) Comparison of shControl, shPhf5a, shPaf1 ESCs, differentiated ESCs and flavopiridol-treated ESCs, respectively. Analysis was performed using the DEGseq25 package.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: ESC shPaf1 WITH LIF

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates. Differentiated cells were cultured in the same conditions in the absence of LIF. ESC strain used: KH2 ESC line (C57BL/6 X 129/Sv) Original ESC reference: Beard, C., et al. (2006). "Efficient method to generate single-copy transgenic mice by site-specific integration in embryonic stem cells." Genesis 44(1): 23-28.

extract_protocol:
Trizol reagent extraction (Invitrogen)
BrUTP labeled nascent RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: ESCs cultured in the presence or absence of LIF, or ESCs treated with flavopiridol (300nM for 1h), or treated with inducible shControl, shPhf5a or shPaf1 knockdown using doxycycline (2μg/mL)


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shControl knockdown treatment replicate 1


title: GRO-Seq analysis in mouse ESCs under shPaf1 knockdown treatment for 3 days replicate 2


title: ChIP-Seq analysis of H3K79me2 in mouse ESCs under shControl knockdown treatment replicate 2


title: SA Lark RNAi Replicate 2


title: GRO-Seq analysis in mouse ESCs under shPaf1 knockdown treatment for 3 days replicate 1


title: MOG KO Treg from MOG immunized mouse – replicate 1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
Data was mapped to mm10 using STAR (v.2.3.1)
Reads that uniquely overlapped UCSC mm10 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package55 (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for exons of UCSC mm10 KnownGenes
Supplementary_files_format_and_content: Normalized read counts expressed in reads per million (RPM) for UCSC mm10 KnownGenes

source_name: Treg cell from lymph nodes

extract_protocol:
Total RNA was isolated using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer V3 kit, briefly, all RNA obtained from 500 cells was used for cDNA synthesis and 15 cycles of PCR were perform to amplify the cDNA. Barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

value: MOG KO


title: ChIP-Seq analysis of H3K4me3 in mouse ESCs under shPhf5a knockdown treatment replicate 2


title: Nipped-B TBPH RNAi Replicate 2


title: Nipped-B TBPH RNAi Replicate 1


title: Lark Mock Replicate 3

value: Mock RNAi treatment


title: MOG KO Treg from MOG immunized mouse – replicate 2


title: MOG KO Treg from MOG immunized mouse – replicate 3


title: Lark Mock Replicate 5


title: WT Treg from MOG immunized mouse – replicate 2


title: GRO-Seq analysis in mouse ESCs under shPhf5a knockdown treatment for 3 days replicate 1

description:
processed_data_file: GRO-SEQ-mESC-shPhf5a-DOX_3days.minus.bw
processed_data_file:  GRO-SEQ-mESC-shPhf5a-DOX_3days.plus.bw


title: Lark Mock Replicate 4


title: TBPH Mock Replicate 4


title: GRO-Seq analysis in mouse ESCs under shControl knockdown treatment for 3 days replicate 3

description:
processed_data_file: GRO-SEQ-mESC-shControl-DOX_3days.minus.bw
processed_data_file:  GRO-SEQ-mESC-shControl-DOX_3days.plus.bw


title: WT Treg from MOG immunized mouse – replicate 3


title: WT Treg from MOG immunized mouse – replicate 1


title: GRO-Seq analysis in mouse ESCs under shPhf5a knockdown treatment for 3 days replicate 2


title: Lark Mock Replicate 1


title: Lark Mock Replicate 2


title: GRO-Seq analysis in mouse ESCs under flavopiridol treatment replicate 3

description:
processed_data_file: GRO-SEQ-mESC-Flavopiridol.minus.bw
processed_data_file:  GRO-SEQ-mESC-Flavopiridol.plus.bw

source_name: ESC WITH LIF


title: TBPH Mock Replicate 3


title: GRO-Seq analysis in mouse ESCs under flavopiridol treatment replicate 2


title: TBPH Mock Replicate 1


title: GRO-Seq analysis in differentiated mouse ESCs replicate 3

description:
processed_data_file: GRO-SEQ-mESC-shControl-NO_LIF_6days.minus.bw
processed_data_file:  GRO-SEQ-mESC-shControl-NO_LIF_6days.plus.bw

source_name: ESC WITHOUT LIF


title: GRO-Seq analysis in mouse ESCs under flavopiridol treatment replicate 1


title: GRO-Seq analysis in mouse ESCs under shPhf5a knockdown treatment for 3 days replicate 3


title: SA Mock Replicate 2


title: SA Mock Replicate 3


title: GRO-Seq analysis in differentiated mouse ESCs replicate 1


title: Nipped-B Mock Replicate 2


title: SA Mock Replicate 1


title: GRO-Seq analysis in mouse ESCs replicate 2

description:
processed_data_file: GRO-SEQ-mESC-shControl-NO_DOX.minus.bw
processed_data_file:  GRO-SEQ-mESC-shControl-NO_DOX.plus.bw


title: GRO-Seq analysis in mouse ESCs replicate 3


title: GRO-Seq analysis in mouse ESCs replicate 1


title: GRO-Seq analysis in mouse ESCs under shControl knockdown treatment for 3 days replicate 2


title: GRO-Seq analysis in differentiated mouse ESCs replicate 2


title: GRO-Seq analysis in mouse ESCs under shControl knockdown treatment for 3 days replicate 1


title: Ser5P Pol II Mock Replicate 2

description: Ser5P.PolII.BG3.Mock.ave.log.enrichment.sgr

value: Ser5P Pol II

tag: antibody vendor/catalog/lot

value: Cell Signaling Technology, P-Rpb1 CTD(S5)  rabbit monoclonal antibody, catalog no. D9N5I, lot 1.


title: Ser5P Pol II Mock Replicate 1


title: Nipped-B Mock Replicate 1


title: Input Replicate 1


title: TBPH Mock Replicate 2


title: POLII_EAF7_2

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped on sacCer3 build using bowtie version 0.12.8.
Duplicated reads were removed using samtools version 0.1.18
Bam files were converted to BigWig using BEDTools version 2.16.2 and the UCSC tool bedGraphToBigWig
Genome_build: sacCer3
Supplementary_files_format_and_content: bw files

organism: Saccharomyces cerevisiae

growth_protocol: Exponentially growing cells in YPD

extract_protocol:
Chromatins were prepared from sonicated cell lysates and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

tag: genotype

value: MYC-Epl1 Yng2-W247A strain

tag: growth conditions

value: untreated cells, normal growth conditions, 30°C, YPD

tag: antibody #lot number


title: POLII_WT_1

value: MYC-Epl1 strain


title: POLII_EAF7_1


title: POLII_YNG2-WA_1

description:
MYC-Epl1
MYC-Epl1 ∆eaf7 strain

value: MYC-Epl1 deltaeaf7 strain


title: POLII_YNG2-WA_EAF7_1

value: MYC-Epl1 delta_eaf7 strain


title: POLII_YNG2-WA_EAF7_2

value: MYC-Epl1 Yng2-W247A delta_eaf7 strain


title: POLII_WT_2


title: Input Replicate 2


title: POLII_YNG2-WA_2

description:
MYC-Epl1
MYC-Epl1 Yng2-W247A ∆eaf7 strain

value: MYC-Epl1 Yng2-W247A deltaeaf7 strain


title: H4_EAF7

extract_protocol:
Chromatins were prepared from sonicated cell lysates and histone-DNA complexes were isolated with specific antibody.
Libraries were performed by McGill' platform service facilities


title: H4_WT


title: H4_YNG2-WA


title: K8ac_YNG2-WA_EAF7


title: K8ac_WT


title: K8ac_YNG2-WA


title: MYC_YNG2-WA_EAF7


title: MYC_WT


title: K8ac_EAF7


title: MYC_Mock

description: No-tag

value: control strain with no MYC tag


title: MYC_EAF7


title: HiChIP oct4 v6.5 biological replicate 1 technical replicate 2

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

institute: Stanford University

description:
Protein-enriched long-range contact.
Processed data file: HiChIP_mES_Oct4.hic

data_processing:
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Processed reads were then inputted into the Juicebox pipeline (PMID: 27467250) to allow for visualization of the interaction matrix.
Genome_build: mm9
Supplementary_files_format_and_content: *allValidPairs.txt: Output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: *hic: Output from the Juicebox pipeline. This file allows for visualization of the interaction matrix.

source_name: v6.5 embryonic stem cell

growth_protocol: mES cells were grown on gelatin plates with serum and LIF.

extract_protocol:
Long-range contacts were generated and ChIP was performed.
Libraries were prepared using the Tn5 transposase.
Nextera

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes.

value: ES cell

tag: gender

value: male


title: HiChIP oct4 v6.5 biological replicate 2 technical replicate 1


title: MYC_YNG2-WA


title: HiChIP oct4 v6.5 biological replicate 1 technical replicate 1


title: HiChIP v6.5 1m technical replicate 2

description:
Protein-enriched long-range contact.
Processed data file: HiChIP_mES_cohesin_all.hic

data_processing:
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908).
Processed reads were then inputted into the Juicebox pipeline (PMID: 27467250) to allow for visualization of the interaction matrix.
Genome_build: hg19,mm9
Supplementary_files_format_and_content: *allValidPairs.txt: Output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: *hic: Output from the Juicebox pipeline. This file allows for visualization of the interaction matrix.

growth_protocol: mES cells were grown on gelatin plates with serum and LIF. GM cells were grown in RPMI-1640 with serum.


title: HiChIP oct4 v6.5 biological replicate 2 technical replicate 2


title: HiChIP v6.5 5m technical replicate 2


title: H4_YNG2-WA_EAF7


title: HiChIP v6.5 1m technical replicate 1


title: HiChIP v6.5 5m technical replicate 1


title: HiChIP v6.5 10m technical replicate 2


title: HiChIP v6.5 biological replicate 2 technical replicate 1


title: HiChIP v6.5 biological replicate 1 technical replicate 2


title: HiChIP v6.5 biological replicate 1 technical replicate 1


title: HiChIP v6.5 biological replicate 2 technical replicate 2


title: HiChIP GM biological replicate 2 technical replicate 1

description:
Protein-enriched long-range contact.
Processed data file: HiChIP_GM_cohesin.hic

value: Lymphoblastoid

value: female


title: HiChIP GM biological replicate 2 technical replicate 2


title: HiChIP GM biological replicate 1 technical replicate 2


title: HiChIP GM biological replicate 1 technical replicate 1


title: LR6_miRNA

status: Public on Aug 30 2016

city: Hangzhou

first: conger

last: lu

address: No.2 Street

institute: zhejiang sci-tech university

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis .
Raw sequencing reads were obtained using the Illumina Pipeline v1.5 software, the processed datas were performed by the Pipeline Firecrest Module and base-calling performed by the Pipeline Bustard Module.
Following the removal of the adapter sequences, low-quality reads, common RNA families (mRNA, rRNA, tRNA, snRNA, and snoRNA) and repeats, the unique reads of 16-29 bases in length were mapped to the pre-microRNA and mature microRNA sequences from Pisces (Danio rerio,  Ictalurus punctatus, Cyprinus carpio, Fugu rubripes, Hippoglossus hippoglossus,  Oryzias latipes,  Tetraodon nigroviridis  and Paralichthys olivaceus), Xenopus laevis, Xenopus tropicalis, Homo sapiens and Mus musculus  listed in miRBase v20.0 (http://www.mirbase.org/) and   the genomes of  C. milii (http://www.ncbi.nlm.nih.gov/genome/?term=Callorhinchus+milii; Callorhinchus_milii-6.1.3) and  L. erinacea  (http://www.ncbi.nlm.nih.gov/genome/?term=Leucoraja+erinacea; LER_WGS_1).
Supplementary_files_format_and_content: abundance measurements

organism: Chiloscyllium plagiosum

source_name: liver of whitespotted bamboo shark

extract_protocol: The total RNA in the Chiloscyllium plagiosum liver was extracted using the Total RNA Purification Kit (LC Sciences) following the manufacturer’s protocol, and the deep sequencing of small RNAs extracted from Chiloscyllium plagiosum liver was performed at LC Sciences using Illumina’s Genome analyzer II platform. Small RNAs were size-fractionated to isolate RNA fragments 15–50 nt long and ligated to SRA5’ adapter , and 41–76 nt long RNA fragments were isolated. This step was followed by SRA3’ adapter ligation and The 64–99 nt long RNA fragments were isolated. The RNAs were converted reverse transcribed to single-stranded cDNAs and then PCR amplified for 20 cycles using Illumina’s small RNA primer set, and cDNA in the 80-115 bp range that contained miRNA was isolated. This fraction was eluted, precipitated and quantified on Nanodrop (Thermo Scientific). The concentration of cDNA sample was adjusted to 10nM and 10 µl was used for sequencing reaction.. Purified cDNA was used for cluster generation on Illumina’s Cluster Station and sequenced using Illumina GAIIx platform Raw sequencing reads were obtained using the Illumina Pipeline v1.5 software following sequencing image analysis by the Pipeline Firecrest Module and base-calling by the Pipeline Bustard Module.

treatment_protocol: A live Chiloscyllium plagiosum was purchased from Shantou aquatic products markets, One-thirds of the liver was surgically removed with 20% urethane (1.25 g per Kg weight of shark) as an anesthetic. The wound was then closed, and the shark was placed into seawater to continue feeding, after 3 h，6 h, 12 h, 24 h, respectively, the liver was surgically removed. These experiments complied with the relevant national animal welfare laws and were conducted under guidelines approved by the China Wildlife Conservation Association.

tag: tissue

value: regenerating liver 6h after partial hepatectomy


title: LN_miRNA

value: normal liver


title: LR12_miRNA

value: regenerating liver 12h after partial hepatectomy


title: LR24_miRNA

value: regenerating liver 24h after partial hepatectomy


title: Notch1-KO_sample1

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

data_processing:
Preliminary processing of raw reads was performed using Casava 1.8 (Illumina).
Adapters and low-quality bases were trimmed using trimmomatic (version 0.23)
Trimmed reads for each sample were aligned to the Mus musculus UCSC mm10 genome using the TopHat version 2.0.10 software package (Bowtie 2 version 2.2.1 software).
Cufflinks software was used to generate assembled transcripts for each group, and the abundance was evaluated using read data.
These assemblies were used with the Cuffdiff tools from the Cufflinks 2.2.1 package to calculate the differential expression levels and to evaluate the statistical significance of the detected alterations.
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel file include FPKM values for all samples

extract_protocol:
The apical and middle turns of at least six cochleae from each group were pooled to isolate the total RNA using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlear

tag: age

value: postnatal 7


title: Notch1-KO_sample3

source_name: apical and middle turns of at least six cochleae


title: LR3_miRNA

value: regenerating liver 3h after partial hepatectomy


title: Control_sample1


title: HepG2 cells treated by control solvent [CON]

first: Ning

last: Wei

address: 320 Yueyang RD.

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH37 whole genome using bowtie MapSplice version 2.1.7.
The stat of mapped reads was list in MappingStatistic_CON.xls and MappingStatistic_S01.xls
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: GRCH37
Supplementary_files_format_and_content: RPKM values for each Sample

source_name: Control HepG2 cells

extract_protocol:
HepG2 cells exposed to low concentration DEHP or control solvent for three months. After that,  the control and DEHP treated cells were collected , and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Lifetech protocol.

tag: tissue source

value: liver

tag: genotype/variation

value: WT control

tag: exposed to

value: control solvent for three months


title: HepG2 cells treated by 0.25 nM DEHP [SO1]

source_name: DEHP treated HepG2 cells

value: low concentration DEHP for 3 months


title: Control_sample2


title: b-catenin-OE and Notch1-KO_sample2


title: HiChIP v6.5 10m technical replicate 1


title: b-catenin-OE_sample2


title: b-catenin-OE and Notch1-KO_sample1


title: 102_3.5_DCA_FFPE

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

data_processing:
After sequencing, basecall files were converted into FASTQ output files using Illumina CASAVA software and other tools developed at EA (available at https://github.com/ExpressionAnalysis/ ea-utils/). FASTQ data were demultiplexed, and sequencing adapters and other low quality bases were clipped to prepare reads for alignment using fastq-mcf --max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25 -l 25
Filtered reads were mapped to mm10.fa using Star 2.4 with parameters --readFilesCommand zcat --chimSegmentMin 15 --chimJunctionOverhangMin 17 --chimScoreMin 1 --chimScoreDropMax 20 --chimScoreSeparation 10 --quantMode TranscriptomeSAM --outSAMattributes NH  --alignSJoverhangMin 8 --sjdbScore 3 --outSAMunmapped Within --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --sjdbOverhang 200
BAM files resulting from Star 2.4 were used as input for rsem-calculate-expression using default parameters.
Raw read counts were normalized across all samples using upper quartile normalization.
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited files with estimated counts for all genes and FPKM normalized counts for all genes

source_name: formalin-fixed paraffin embedded left lateral and right media liver lobes

growth_protocol: Studies were conducted in 4 week-old male B6C3F1 mice maintained under standard housing conditions at the U.S. Environmental Protection Agency (US EPA) AAALAC-accredited animal facility (Research Triangle Park, NC). Animal care and procedures were conducted under protocols approved by the Institutional Animal Care and Use Committee of the USEPA.

extract_protocol:
For liquid nitrogen frozen (FROZ) liver samples, ~20 mg of liver tissue per sample was homogenized in RNAzol®RT , purified with the Qiagen RNeasy MinElute column protocol, evaluated for integrity using an Agilent 2100 Bioanalyzer, and quantitated using a Qubit fluorometer. For FFPE liver samples, four 10-μm sections were collected from each tissue block using a Leica RM 2155 microtome. FFPE sample were deparaffinized using Qiagen Deparaffinization Solution and RNA isolated and purified according to Qiagen AllPrep DNA/RNA FFPE Kit protocol. FFPE RNA quantitated as for FROZ samples.
Total RNA was converted into cDNA libraries using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit (#RS-122-2303, Illumina, San Diego, CA). Briefly, ribosomal RNA (rRNA) was removed from 100 ng of total RNA by hybridization to a biotinylated probe selective for rRNA species, followed by streptavidin bead binding, purification, and fragmentation by heat in the presence of divalent cations. Double-stranded cDNA was generated by removing the RNA template and synthesizing the second strand with dUTP in place of dTTP. A single ‘A’ base was added to the 3’ end to facilitate ligation of sequencing adapters, which contained a single ‘T’ base overhang. Adapter-ligated cDNA was amplified by polymerase chain reaction (PCR) to increase the amount of sequence-ready library. During this amplification the polymerase stalls when it encounters a ‘U’ base, rendering the second strand a poor template. The first strand thus serves as template for amplified sequence, preserving strand information. Final cDNA libraries were analyzed for size distribution and integrity using an Agilent Bioanalyzer (DNA 1000 kit #5067-1504), quantitated by qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA), and normalized to 2 nM in preparation for sequencing.Samples were sequenced at EA Genomics (Q2 Solutions, Durham, NC) using the Illumina HiSeq platform

treatment_protocol: DEHP (CAS No: 117-81-7; 99.5% purity, Chem Service) was administered in the feed for 7 days at dietary doses of 0, 1500, 3000, and 6000 ppm (as described in Lake et al. 2015). Dichloroacetic acid (CAS 79-43-6, Aldrich) was administered in the drinking water at doses of 0, 1.0, 2.0, and 3.5 g/L (as described in DeAngelo et al. 1991).

tag: sample preparation

value: formalin-fixed paraffin embedded

value: 4 weeks

tag: Sex

value: dichloroacetic acid (DCA)

tag: dose


title: b-catenin-OE_sample1


title: 101_3.5_DCA_FFPE

tag: strain

value: male


title: 100_3.5_DCA_FFPE

tag: treatment


title: b-catenin-OE_sample3


title: 99_3.5_DCA_FFPE


title: 78_2_DCA_FFPE

value: 2 g/L


title: 97_3.5_DCA_FFPE