title: 393 TUDCA + Tg 4h

description:
test
TUDCA + Tg 4h

value: TUDCA plus Thapsigargin

value: Healthy donor


title: 109 point zero

status: Public on Jan 19 2020

type: RNA

city: São Paulo

first: Maristela

middle: Martins de

last: Camargo

state: SP

address: Av. Prof. Lineu Prestes 1730

department: Immunology

country: Brazil

institute: University of São Paulo

description:
control
point zero

data_processing: Target DCq values were normalized against Gapdh DCq levels. Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_GAPDH)]. Replicates were averaged and filtered for SE < 0.5 for removal os low-abundance measurements. A ratio of Treated (x) / Untreated (NT) was calculated and log2-transformed.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: EBV-immortalized B cell

label_protocol: All RNA samples were normalized to 30 ng/ul before proceeding. cDNA was generated using 300 ng of total RNA and the High-Capacity RNA-to-cDNA kit (Thermo Scientific). cDNA was ketp at -20˚C until processing. Thirty-three nL of TaqMan OpenArray Real-Time PCR Master Mix (Thermo Scientific) were loaded into custom-made TaqManOpenArray slides by an automated Accufill system (Thermo Scientific) and amplified in triplicate reactions for quantification of specific transcipts using a QuantStudio 12K Flex real-Time PCR System (Thermo Scientific) for up to 40 cycles.

growth_protocol: EBV-B cells were cultured in RPMI-1640 GlutaMAX media containing 100U/ml penicollon, 100ug/ml streptomycin and 10% heat-inactivated fetal bovine serum (all from Thermo Scientific) at 37˚C and 5% CO2. Cells were split every 3 days, and harvested for experiments between the 3rd and 10th splits. Cell vioability was determined by Trypan blue staining using an automatic counter Countess II (Thermo Scientific).

extract_protocol: Samples were harvested in RNAlater (Thermo Scientific) and kept at -20˚C until processing. Total RNA was isolated using Purelink Mini (thermo Scientific) and kept at -80˚C until processing. Purified RNA was quali- and quantified by spectrometry in a Nanodrop and by fluorometry in a Qubit, respectively.

treatment_protocol: Cells were plated as triplicates at 3x10e5 cells/well (96 round bottom plate) in media containing chemical chaperones (final concentrations were 1 mM PBA, 5 mM TUDCA, or 1 mM DMSO) and/or ER stressors (final concentrations were 1uM Thapsigargin (Tg) or 10 ug/ml Tunicamycin (Tm). Cells were stimulated for 1, 2, 3 and 4 hours (h) or left untreated.

tag: time

value: 0 hour (fresh)

tag: treatment

value: no treatment

tag: cell lineage origin

value: Patient P1


title: NTX9415sc_58

type: SRA

city: Berlin

first: Annika

last: Fendler

address: Robert-Roessle-Str. 10

department: Signal Transduction in Development and Cancer

country: Germany

institute: Max Delbrueck Center for Molecular Medicine in the Helmholtz Association

library_source: transcriptomic

data_processing:
Conversion and demultiplexing with BCL2FASTQ (v2.20)
Demultiplexing, alignment and generation of a UMI count matrix with CELSEQ2
Normalisation and cluster analysis with Seurat (V2.2.0)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Raw UMI  read counts in a .csv format generated with CELSEQ2

molecule: polyA RNA

source_name: Single Cell data of patient NTX9415

extract_protocol:
Single CXCR4+MET+CD44+ cells were sorted into 96-well plates into lysis buffer.
SuperScript II double-stranded cDNA Synthesis kit (Thermo Fisher) was used for reverse transcription. ERCC spike-in (Thermo Fisher) was added to the primer mix. AmPure XP kit (Beckman Coulter) was used for RNA clean-up. In vitro transcription was performed using the MEGAscript T7 transcription kit  (Thermo Fisher). aRNA was transcribed to cDNA using random hexamer primers and SuperscriptII polymerase (Invitrogen) and amplified using RP1 Illumina Primers.

tag: cell type

value: clear cell renal cell cancer

tag: patient id


title: NTX9415sc_60


title: NTX9415sc_59


title: NTX9415sc_55


title: 395 TUDCA + Tn 4h

description:
test
TUDCA + Tn 4h

value: 4 hours

value: TUDCA plus Tunicamycin


title: NTX9415sc_57


title: NTX9415sc_68


title: 390 TUDCA + Tn 3h

description:
test
TUDCA + Tn 3h

value: 3 hours


title: NTX9415sc_54


title: 388 TUDCA + Tg 3h

description:
test
TUDCA + Tg 3h


title: NTX9415sc_53


title: 387 TUDCA + Tg 3h

description:
test
TUDCA + Tg 3h


title: NTX9415sc_52


title: NTX9415sc_51


title: 386 TUDCA + Tg 3h

description:
test
TUDCA + Tg 3h


title: NTX9415sc_50


title: NTX9415sc_61


title: 384 TUDCA + Tn 2h

description:
test
TUDCA + Tn 2h

value: 2 hours


title: 392 TUDCA + Tg 4h

description:
test
TUDCA + Tg 4h


title: NTX9415sc_49


title: NTX9415sc_48


title: 381 TUDCA + Tg 2h

description:
test
TUDCA + Tg 2h


title: NTX9415sc_47


title: 385 TUDCA + Tn 2h

description:
test
TUDCA + Tn 2h


title: 380 TUDCA + Tn 1h

description:
test
TUDCA + Tn 1h

value: 1 hour


title: NTX9415sc_46


title: 379 TUDCA + Tn 1h

description:
test
TUDCA + Tn 1h


title: NTX9415sc_42


title: NTX9415sc_43


title: NTX9415sc_44


title: 377 TUDCA + Tg 1h

description:
test
TUDCA + Tg 1h


title: 391 TUDCA + Tg 4h

description:
test
TUDCA + Tg 4h


title: NTX9415sc_45


title: 376 TUDCA + Tg 1h

description:
test
TUDCA + Tg 1h


title: NTX9415sc_41


title: 378 TUDCA + Tg 1h

description:
test
TUDCA + Tg 1h


title: 374 TUDCA 4h

description:
test
TUDCA 4h

value: TUDCA


title: NTX9415sc_40


title: NTX9415sc_39


title: 373 TUDCA 4h

description:
test
TUDCA 4h


title: 372 DMSO + Tn 4h

description:
test
DMSO + Tn 4h

value: DMSO plus Tunicamycin


title: 383 TUDCA + Tg 2h

description:
test
TUDCA + Tg 2h


title: 371 DMSO + Tn 4h

description:
test
DMSO + Tn 4h


title: 370 DMSO + Tn 4h

description:
test
DMSO + Tn 4h


title: NTX9415sc_35


title: NTX9415sc_36


title: NTX9415sc_37


title: 369 TUDCA 3h

description:
test
TUDCA 3h


title: 368 TUDCA 3h

description:
test
TUDCA 3h


title: NTX9415sc_33


title: 367 TUDCA 3h

description:
test
TUDCA 3h


title: 366 DMSO + Tn 3h

description:
test
DMSO + Tn 3h


title: NTX9415sc_32


title: NTX9415sc_30


title: 375 TUDCA 4h

description:
test
TUDCA 4h


title: NTX9415sc_29


title: NTX9415sc_34


title: NTX9415sc_28


title: 363 TUDCA 2h

description:
test
TUDCA 2h


title: 365 DMSO + Tn 3h

description:
test
DMSO + Tn 3h


title: 362 TUDCA 2h

description:
test
TUDCA 2h


title: 364 DMSO + Tn 3h

description:
test
DMSO + Tn 3h


title: 361 DMSO + Tn 2h

description:
test
DMSO + Tn 2h


title: NTX9415sc_27


title: NTX9415sc_26


title: NTX9415sc_38


title: 360 DMSO + Tn 2h

description:
test
DMSO + Tn 2h


title: NTX9415sc_31


title: 359 DMSO + Tn 2h

description:
test
DMSO + Tn 2h


title: NTX9415sc_25


title: NTX9415sc_24


title: 358 TUDCA 1h

description:
test
TUDCA 1h


title: NTX9415sc_23


title: 356 DMSO + Tn 1h

description:
test
DMSO + Tn 1h


title: NTX9415sc_21


title: 355 DMSO + Tn 1h

description:
test
DMSO + Tn 1h


title: 354 DMSO + Tg 4h

description:
test
DMSO + Tg 4h

value: DMSO plus Thapsigargin


title: NTX9415sc_20


title: 352 DMSO + Tg 4h

description:
test
DMSO + Tg 4h


title: NTX9415sc_17


title: 353 DMSO + Tg 4h

description:
test
DMSO + Tg 4h


title: 350 DMSO 4h

description:
test
DMSO 4h

value: DMSO


title: 349 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: NTX9415sc_19


title: 347 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: NTX9415sc_18


title: 348 DMSO + Tg 3h

description:
test
DMSO + Tg 3h


title: NTX9415sc_16


title: 346 DMSO 3h

description:
test
DMSO 3h


title: NTX9415sc_15


title: NTX9415sc_10


title: NTX9415sc_12


title: 344 DMSO + Tg 2h

description:
test
DMSO + Tg 2h


title: NTX9415sc_11


title: NTX9415sc_14


title: 357 TUDCA 1h

description:
test
TUDCA 1h


title: NTX9415sc_22


title: NTX9415sc_9


title: 343 DMSO 2h

description:
test
DMSO 2h


title: NTX28214sc_5

source_name: Single Cell data of patient NTX28214


title: 342 DMSO + Tg 1h

description:
test
DMSO + Tg 1h


title: NTX9415sc_7


title: 351 DMSO 4h

description:
test
DMSO 4h


title: 340 DMSO 1h

description:
test
DMSO 1h


title: 339 PBA + Tn 4h

description:
test
PBA + Tn 4h

value: 4-PBA plus Tunicamycin


title: NTX9415sc_13


title: 338 PBA + Tn 4h

description:
test
PBA + Tn 4h


title: NTX9415sc_5


title: 337 PBA + Tn 4h

description:
test
PBA + Tn 4h


title: NTX9415sc_3


title: NTX9415sc_4


title: 336 PBA + Tg 4h

description:
test
PBA + Tg 4h

value: 4-PBA plus Thapsigargin


title: NTX9415sc_2


title: 345 DMSO + Tg 2h

description:
test
DMSO + Tg 2h


title: NTX9415sc_1


title: 335 PBA + Tg 4h

description:
test
PBA + Tg 4h


title: 333 PBA + Tn 3h

description:
test
PBA + Tn 3h


title: 332 PBA + Tn 3h

description:
test
PBA + Tn 3h


title: 331 PBA + Tn 3h

description:
test
PBA + Tn 3h


title: LS-165_DMSO

city: Bergen

first: Laurence

middle: William-Joseph

last: Dyer

address: Haukelandsveien 22

department: Clinical Institute

country: Norway

institute: University of Bergen

data_processing:
Illumina Casava v1.8
Reads were aligned to the Human reference genome (GrCH38) using HiSat (Version 2.10.0), with options “hisat2-align-s --wrapper basic-0 -p 140”
Aligned reads were then put into featureCounts (Version 1.5.2) with options “featureCounts -T 64 -p -t exon -g gene_id”
Differential expression analysis was performed via DESeq2 (Version 1.14.1)
Genome_build: GrCH38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 normalised counts for each Sample ...

source_name: Adipose

growth_protocol: The stromal vascular fraction (SVF) from subcutaneous adipose tissue was isolated as previously described (Lee and Fried, 2014) with some modifications. Briefly, KRP-buffer containing Liberase Blendzyme 3 (Roche) and DNase was used to enzymatically digest the liposuction aspirate. Following a 1-hour incubation at 37°C, the digested fat tissue was filtered and the SVF was extracted by repetitive washing with 0.9% NaCl followed by pelleting cells by centrifugation. Red blood cells were lysed using a buffer containing NH 4 Cl (155 mM), K 2 HPO 4 (5.7 mM) and EDTA (0.1 mM). Thereafter, SVF was cultured in GlutaMAX DMEM (Thermo Fisher) supplemented with 10% fetal bovine serum (FBS) and 50 μg/ml gentamicin (Sigma) and grown at 37°C with 5% CO 2 . Adipocyte progenitor cells were counted before seeding. The day after seeding of isolated SVF, adipogenic differentiation was induced by supplementing the culture medium with 33 μM biotin, 1 nM triiodothyronine, 17 μM DL-pantothenate, 10 μg/ml transferrin, 66 nM insulin, 100 nM cortisol, 15 mM Hepes and 10 μM rosiglitazone. Rosiglitazone was discontinued after 6 days and terminal differentiation was defined at 12-13 days.

extract_protocol:
Total RNA from human cell cultures was obtained using RNeasy kit (QIAGEN) and quality checked by QIAxpert spectrophotometer (QIAGEN) prior to cDNA synthesis with 200 ng RNA input using a high-capacity cDNA reverse transcription kit (Applied Biosystems). Sample cDNA was analyzed by Lightcycler480 (Roche) quantitative real-time PCR using SYBR Green dye (Roche) and target primers (Table S3). Relative mRNA expression was determined by standard curves and normalized to reference genes (Table S3) as indicated. qPCR was performed with duplicate technical reactions per biological sample and averaged for further analyses.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Individuals were treated with either BMS or DMSO (vehicle).

tag: age

value: 12 days

tag: patient


title: LS-165_BMS

value: BMS


title: NTX9415sc_8


title: 341 DMSO + Tg 1h

description:
test
DMSO + Tg 1h

value: Healthy donor


title: 330 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: LS-166_BMS


title: LS-163_BMS


title: NTX9415sc_6


title: LS-166_DMSO


title: LS-162_DMSO


title: 328 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: 329 PBA + Tg 3h

description:
test
PBA + Tg 3h


title: LS-163_DMSO


title: LS-162_BMS


title: 326 PBA + Tn 2h

description:
test
PBA + Tn 2h


title: 325 PBA + Tn 2h

description:
test
PBA + Tn 2h


title: 324 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: 323 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: LS-161_BMS


title: LS-161-DMSO


title: LS-159_DMSO


title: 322 PBA + Tg 2h

description:
test
PBA + Tg 2h


title: LS-159_BMS


title: 334 PBA + Tg 4h

description:
test
PBA + Tg 4h


title: 321 PBA + Tn 1h

description:
test
PBA + Tn 1h


title: BS_clr4∆uhf1∆

city: SAN FRANCISCO

first: Hiten

last: Madhani

state: CA

country: USA

institute: University of California San Francisco

description:
Genomic DNA
BS-clr4-uhrf08.CGmap.csv.gz

library_source: genomic

data_processing:
ChIP-seq and methyl-seq
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom scripts
bisulfite-seq:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned  using Bismark (Krueger et al. 2011)  and BSseeker2 (Guo et al., 2013)
Analysis performed using custom scritps to compare technical replicates
Supplementary_files_format_and_content: "CGmap.csv": contain output for bisulfite sequence with the position of each 5mC in the genome as per BSseeker output format (Guo et al., 2013)
Supplementary_files_format_and_content: .bedgraph: Signal of methyl-seq of the  sample normalised to  methyl-seq signal in dnmt5∆
Supplementary_files_format_and_content: .csv : comparison of the ChIP-seq signal from different samples
Genome_build: C. neoformans CNA3
Genome_build: C45 (BioProject PRJNA517966)
Genome_build: A1_35_8(BioProject PRJNA517966)
Genome_build: A5_35_17(BioProject PRJNA517966)
Genome_build: Bt106(BioProject PRJNA517966)
Genome_build: Bt88(BioProject PRJNA517966)
Genome_build: Ze90(BioProject PRJNA517966)
Genome_build: Ftc146_1(BioProject PRJNA517966)
Genome_build: PMHc1023.ENR(BioProject PRJNA517966)

molecule: genomic DNA

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: Samples were inoculated from saturated starter cultures in YPAD at 30C until reaching OD 1.0 then harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
Genomic DNA was extracted as described in Chun and Madhani, Methods Enzym. 2010.
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by antibodies directed to our proteins of interest (10 mg of anti-Histone H3, 10 mg anti-FLAG M2, or 4 mg of anti-Cse4).  DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
ChIP-seq: Described in Homer et al. 2016
Bisulfite-seq: Described in Urich et al., 2015
MeDIP-seq: the initial step as described in Urich et al., 2015 with the exception that unmethylated adapters were ligated to repaired, dA-tailed DNA.

treatment_protocol:
NA
Induction: Upon transformation, cells were selected in YPAD+nourseothrycin and then propagated for two sequential single-colony streaks in presence of galactose to induce DnmtX.
Time course: Wild-type cells from a starter culture (g0) were propagated at 30°C in rich media for 120 generations maintaining the logarithmic growth by diluting the culture as soon as it reached an OD600 of 1. After 120 generations, the cells were plated on YPAD agar plates to form single colonies at 30°C. Two independent isolates (colony 1 and colony 2) were grown overnight in rich media to OD600 of 1 and the genomic DNA extracted processed in technical duplicates for WGBS

tag: strain

tag: genotype

tag: antibody


title: BS_clr4∆

description:
Genomic DNA
BS-clr4.CGmap.csv.gz


title: 320 PBA + Tn 1h

description:
test
PBA + Tn 1h


title: BS_uhf1∆

description:
Genomic DNA
BS-uhrf108.CGmap.csv.gz


title: BS_wild type

description:
Genomic DNA
BS-wt.CGmap.csv.gz

value: wild type


title: 319 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 318 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 317 PBA + Tg 1h

description:
test
PBA + Tg 1h


title: 316 PBA 4h

description:
test
PBA 4h


title: 315 PBA 4h

description:
test
PBA 4h


title: 314 PBA 4h

description:
test
PBA 4h


title: MeDIP-RI

description:
Affinity purified DNA
MeDIP-RI.bedgraph


title: MeDIP-SC341

description:
Affinity purified DNA
MeDIP-SC341_S15_R1_001.bedgraph

treatment_protocol:
Induction
Induction: Upon transformation, cells were selected in YPAD+nourseothrycin and then propagated for two sequential single-colony streaks in presence of galactose to induce DnmtX.
Time course: Wild-type cells from a starter culture (g0) were propagated at 30°C in rich media for 120 generations maintaining the logarithmic growth by diluting the culture as soon as it reached an OD600 of 1. After 120 generations, the cells were plated on YPAD agar plates to form single colonies at 30°C. Two independent isolates (colony 1 and colony 2) were grown overnight in rich media to OD600 of 1 and the genomic DNA extracted processed in technical duplicates for WGBS


title: MeDIP-SC347

description:
Affinity purified DNA
MeDIP-SC347_S14_R1_001.bedgraph


title: MeDIP-wt

description:
Affinity purified DNA
MeDIP_wt.bedgraph


title: 327 PBA + Tn 2h

description:
test
PBA + Tn 2h


title: MeDIP-delta

description:
Affinity purified DNA
MeDIP-Dnmt5delta_S7_R1_001.bedgraph


title: MeDIP-SC351

description:
Affinity purified DNA
MeDIP-SC351_S16_R1_001.bedgraph


title: 313 Tn 4h

description:
test
Tn 4h

value: Tunicamycin


title: 311 Tn 4h

description:
test
Tn 4h


title: 312 Tn 4h

description:
test
Tn 4h


title: 310 PBA 3h

description:
test
PBA 3h


title: 309 PBA 3h

description:
test
PBA 3h


title: 308 PBA 3h

description:
test
PBA 3h


title: K9_dmt5∆-2

description:
Affinity purified DNA
H3K9_ChIP_wt_vs_Dnmt5del.csv


title: K9_RI-DMT5-1

description:
Affinity purified DNA
H3K9_ChIP_WT_vs_RI.csv


title: K9_dmt5∆-1


title: K9_wt1


title: 307 Tn 3h

description:
test
Tn 3h


title: 306 Tn 3h

description:
test
Tn 3h


title: H3_wt2


title: 304 PBA 2h

description:
test
PBA 2h


title: H3_RI-DMT5-1


title: H3_dmt5∆-2


title: 303 PBA 2h

description:
test
PBA 2h


title: 302 PBA 2h

description:
test
PBA 2h


title: H3_dmt5∆-1


title: FLAG_WCE

description:
Genomic DNA
FLAG_ChIP.csv


title: FLAG_untag

description:
Affinity purified DNA
FLAG_ChIP.csv

value: anti-FLAG


title: 300 Tn 2h

description:
test
Tn 2h


title: FLAG_RI-DMT5-2

description:
Affinity purified DNA
FLAG_ChIP.csv


title: K9_wt2


title: K9_RI-DMT5-2


title: 298 PBA 1h

description:
test
PBA 1h


title: FLAG_RI-DMT5-1

description:
Affinity purified DNA
FLAG_ChIP.csv


title: 299 Tn 2h

description:
test
Tn 2h


title: 297 PBA 1h

description:
test
PBA 1h


title: FLAG-DMT5_2

description:
Affinity purified DNA
FLAG_ChIP.csv


title: FLAG-DMT5_1

description:
Affinity purified DNA
FLAG_ChIP.csv


title: 296 PBA 1h

description:
test
PBA 1h


title: BS_PMHc1023_rep2

description:
Genomic DNA
CM1883_Compare.CGmap.csv


title: 295 Tn 1h

description:
test
Tn 1h


title: 294 Tn 1h

description:
test
Tn 1h


title: 305 Tn 3h

description:
test
Tn 3h


title: BS_Ftc146_rep2

description:
Genomic DNA
CM1882_Compare.CGmap.csv


title: BS_Ftc146_rep1

description:
Genomic DNA
CM1882_Compare.CGmap.csv


title: 292 Tg 4h

description:
test
Tg 4h

value: 4 hours

value: Thapsigargin


title: H3_wt1


title: 293 Tn 1h

description:
test
Tn 1h


title: BS_Ze90_rep1

description:
Genomic DNA
CM1880_Compare.CGmap.csv


title: BS_Ze90_rep2

description:
Genomic DNA
CM1880_Compare.CGmap.csv


title: 301 Tn 2h

description:
test
Tn 2h


title: 290 Tg 4h

description:
test
Tg 4h


title: 291 Tg 4h

description:
test
Tg 4h


title: 289 NT 4h

description:
control
NT 4h

value: no treatment


title: 288 NT 4h

description:
control
NT 4h


title: BS_Bt88_rep1

description:
Genomic DNA
CM1879_Compare.CGmap.csv


title: 286 Tg 3h

description:
test
Tg 3h

value: 3 hours


title: BS_Bt106_rep2

description:
Genomic DNA
CM1878_Compare.CGmap.csv


title: BS_Bt106_rep1

description:
Genomic DNA
CM1878_Compare.CGmap.csv


title: 285 Tg 3h

description:
test
Tg 3h


title: BS_A5_35_17_rep2

description:
Genomic DNA
CM1877_Compare.CGmap.csv


title: 284 Tg 3h

description:
test
Tg 3h


title: 287 NT 4h

description:
control
NT 4h


title: 283 NT 3h

description:
control
NT 3h


title: 282 NT 3h

description:
control
NT 3h


title: BS_PMHc1023_rep1

description:
Genomic DNA
CM1883_Compare.CGmap.csv


title: BS_A1_35_8_rep1

description:
Genomic DNA
CM1876_v2_Compare.CGmap.csv.gz


title: BS_A5_35_17_rep1

description:
Genomic DNA
CM1877_Compare.CGmap.csv


title: 281 NT 3h

description:
control
NT 3h


title: BS_A1_35_8_rep2


title: BS_C45_rep2

description:
Genomic DNA
CM1875_Compare.CGmap.csv


title: 280 Tg 2h

description:
test
Tg 2h

value: 2 hours


title: BS_C45_rep1

description:
Genomic DNA
CM1875_Compare.CGmap.csv


title: 279 Tg 2h

description:
test
Tg 2h


title: 278 Tg 2h

description:
test
Tg 2h


title: BS_W0_g0_1

description:
Genomic DNA
W0_1_SE_noMM_PacBio.CGmap.csv

treatment_protocol:
time course
Induction: Upon transformation, cells were selected in YPAD+nourseothrycin and then propagated for two sequential single-colony streaks in presence of galactose to induce DnmtX.
Time course: Wild-type cells from a starter culture (g0) were propagated at 30°C in rich media for 120 generations maintaining the logarithmic growth by diluting the culture as soon as it reached an OD600 of 1. After 120 generations, the cells were plated on YPAD agar plates to form single colonies at 30°C. Two independent isolates (colony 1 and colony 2) were grown overnight in rich media to OD600 of 1 and the genomic DNA extracted processed in technical duplicates for WGBS


title: 276 NT 2h

description:
control
NT 2h


title: 277 NT 2h

description:
control
NT 2h


title: BS_colony2_2

description:
Genomic DNA
W2_2_SE_noMM_PacBio.CGmap.csv


title: BS_W0_g0_2

description:
Genomic DNA
W0_2_SE_noMM_PacBio.CGmap.csv


title: BS_Bt88_rep2

description:
Genomic DNA
CM1879_Compare.CGmap.csv


title: BS_colony1_2

description:
Genomic DNA
W1_2_SE_noMM_PacBio.CGmap.csv


title: 274 Tg 1h

description:
test
Tg 1h

value: 1 hour


title: BS_K_pini

description:
Genomic DNA
BS_SC347.CGmap.cvs


title: BS_colony1_1

description:
Genomic DNA
W1_1_SE_noMM_PacBio.CGmap.csv


title: 272 Tg 1h

description:
test
Tg 1h


title: BS_K_best

description:
Genomic DNA
BS_SC351.CGmap.csv


title: 273 Tg 1h

description:
test
Tg 1h


title: BS_K_mangro

description:
Genomic DNA
BS_SC341.CGmap.csv


title: BS_colony2_1

description:
Genomic DNA
W2_1_SE_noMM_PacBio.CGmap.csv


title: 271 NT 1h

description:
control
NT 1h


title: 270 NT 1h

description:
control
NT 1h


title: BS_RI-DMT5-2b

description:
Genomic DNA
BS-SC375_2.CGmap.csv


title: BS_RI-DMT5-1b

description:
Genomic DNA
BS-SC374_2.CGmap.csv


title: 268 point zero

description:
control
point zero

value: 0 hour (fresh)


title: 275 NT 2h

description:
control
NT 2h


title: 267 point zero

description:
control
point zero


title: BS_RI-DMT5-1a

description:
Genomic DNA
BS-SC374_1.CGmap.csv


title: BS_dmt5∆-2

description:
Genomic DNA
BS-362_2.CGmap.csv


title: Wild type lens RNA-seq 2

city: Chapel Hill

first: David

last: Corcoran

state: NC

address: 125 Mason Farm Rd

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were trimmed with trim_galore
Reads were mapped using the STAR alignment algorithm
Gene expression was quantified using HTSeq
Genes that had fewer than 10 reads in any one condition were filtered out
Normalization and differential expression were carried out using DESeq2
Genome_build: mm10 with v73 of the Ensembl transcriptome
Supplementary_files_format_and_content: Tab separated text file containing the Ensembl gene IDs and the DESeq2 normalized expression values

organism: Mus musculus

source_name: Wild type lens RNA-seq

extract_protocol:
RNA was isolated using the RNeasy Micro kit
Stranded mRNA seq libraries were constructed using the Kapa kit

treatment_protocol: The S100A4 KO line of mouse used in this study was maintained on a C57BL/6J background and has been thoroughly characterized previously

tag: strain background

tag: genotype/variation

value: Wild-type

tag: tissue

value: lens


title: Wild type lens RNA-seq 1


title: S100A4 null lens RNA-seq 1

source_name: S100A4 null lens RNA-seq

value: S100A4 null


title: 266 point zero

description:
control
point zero


title: S100A4 null lens RNA-seq 2


title: 269 NT 1h

description:
control
NT 1h


title: BS_dmt5∆-1

description:
Genomic DNA
BS-362_1.CGmap.csv


title: DNA_Methylation_EpiSCs_male_p19_B6D2_FT1_873

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing:
FASTQ sequence files were aligned using RMAPBS (Smith et al., 2009; Song et al., 2013) allowing a maximum of 10 mismatches for efficient mapping of reads containing bisulfite converted unmethylated cytosines. Cytosine methylation levels were determined using the standard new pipeline within RMAPBS (Methpipe: Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLOS ONE 8(12): e81148).
In short, both mates of the paired-end sequencing were mapped separately by RMAPBS. If mated reads mapped within 300 bp, the reads were merged and included for analysis. Mated reads mapping with a distance of more than 300 bp were excluded from further analysis. Mated reads mapped within 300 bp, but mapping equally well on multiple positions on the genome, were discarded. If multiple mated reads mapped on exactly the same genomic coordinates, all but one (at random) were discarded. Symmetric cytosines (within a CpG context) on both forward and reverse strands were combined. Cytosine methylation level was called per individual C as: #C/(#C+#T).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: 29_EpiSC_8.73_merged.rmDup.methcounts.bed: Coverage over the cytosines within CpG context are present in the methcounts bed file 4th column. Cytosine methylation levels within CpG context are present in the methcounts bed file 5th column. This files can be used as table, but can also be directly uploaded in the UCSC genome browser.

source_name: Epiblast Stem cells

growth_protocol: EpiSCs were cultured feeder-free in defined CDM medium (Brons et al. 2007) supplemented with 20 ng/mL Activin A and 12 ng/mL Fibroblast growth factor 2 (FGF2).

extract_protocol:
Genomic DNA was purified using DNA extraction kit (Promega) according to the manufacturer’s instructions.
Library construction was performed according to Kulis et al. (2012; Nature Genetics). In short: We spiked genomic DNA (1 or 2 μg) with unmethylated λ DNA (5 ng of λ DNA per μg of genomic DNA) (Promega). We sheared DNA by sonication to 50–500 bp with a Covaris E220 and selected 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience Corp.). We constructed genomic DNA libraries using the TruSeq Sample Preparation kit (Illumina Inc.) following the Illumina standard protocol: the ends of the fragments were repaired, an adenine was added at the 3′ extremities of the fragments and Illumina TruSeq adapters were ligated at each extremity. After adaptor ligation, we treated DNA with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer’s instructions for formalin-fixed and paraffin-embedded (FFPE) tissue samples. We performed two rounds of conversion to get >99% conversion. We enriched adaptor-ligated DNA through seven cycles of PCR using the PfuTurboCx Hotstart DNA polymerase (Stratagene). We monitored library quality using the Agilent 2100 BioAnalyzer (Agilent) and determined the concentration of viable sequencing fragments (molecules carrying adapters at both extremities) by quantitative PCR using the Library Quantification Kit from KAPA Biosystem. We performed paired-end DNA sequencing (two reads of 100 bp each) using the Illumina Hi-Seq 2000.

tag: strain/background

value: Epiblast Stem Cells (EpiSCs)

tag: measurement

value: DNA methylation


title: BS_RI-DMT5-2a

description:
Genomic DNA
BS-SC375_1.CGmap.csv


title: HepG2.2.15-shC2 cells, rep1

status: Public on Jan 18 2020

city: Guangzhou

first: Gang

last: Ning

state: Guangdong

address: 600 Tianhe Road, Guangzhou

department: Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-Sen University

country: China

institute: sun yat-sen university

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes Count values for each Sample

source_name: C2-overexpressing HepG2.2.15 cells

growth_protocol: HepG2.215 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Invitrogen, Carlsbad, USA) supplemented with 10% fetal bovine serum and  100 m/ml penicillin-streptomycin mixture(Invitrogen, America) at 37°C and 5% CO2.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with TruSeq RNA sample Preparation kit V2 in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: First, C2-overexpressing HepG2.2.15 cells (HepG2.2.15-shC2) and HepG2.2.15-mock cells were established following manufacturer’s protocol. Then 2x10e5 HepG2.2.15-shC2 (n=3) and 2x10e5 HepG2.2.15-mock cells (n=3) were seeded in 6-well plates and inoculated for 48 hours, and total RNA was isolated from cell samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).

tag: cell line

value: HepG2.2.15 cells

value: primary HCC cells

value: infected with lentivirus packaged with C2 overexpression plasmid

value: overexpression of Complement 2


title: HepG2.2.15-mock cells, rep2

source_name: HepG2.2.15-mock cells

value: untreated

value: control


title: HepG2.2.15-mock cells, rep3


title: HepG2.2.15-shC2 cells, rep3

description: Sample 6


title: HepG2.2.15-mock cells, rep1


title: Spheres from ccRCC10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile normalized in Partek

label: Biotin

source_name: human clear cell renal cell cancer

label_protocol: Labeling was performed with the Illumina TotalPrep RNA Amplification Kit (Life Technologies)

growth_protocol: Tumor cell suspensions at 100,000 cells/ml were seeded as non-adherent cultures in Poly-HEMA pretreated 24-well plates in DMEM/F12 supplemented with 10 ng/ml EGF, 125 ng/ul FGF, 80 ng/µl Heparin, 1x B27, 1x Penicillin/Streptomycin, and 2.5 µg/ml Amphotericin B.

extract_protocol: Total RNA was isolated from non-cultured, CXCR4+MET+CD44+ or sphere cells using the RNeasy Mini Kit (Qiagen)

tag: gender

value: Male

tag: disease state

value: clear cell renal cell cancer

tag: individual

value: ccRCC patient 10

tag: tnm classification

value: pT3aG2R0L1V2M1 (pul)

value: Spheres


title: Spheres from ccRCC2

value: ccRCC patient 2

tag: cell type


title: Non-cultured cells from ccRCC4

value: ccRCC patient 4

value: Non-cultured cells


title: CXCR4+MET+CD44+ cells from ccRCC4

value: CXCR4+MET+CD44+ cells


title: Spheres from ccRCC4


title: Non-cultured cells from ccRCC10


title: d15_ev_R4

city: Mainz

first: Holger

last: Richly

address: Ackermannweg 4

institute: Institute of molecular Biology

description: Control (EV) treated day 15 replicate 4

data_processing:
Libraries were sequenced on a HiSeq2500 with readlength 51 single reads. Basecalling and demultiplexing was done using bcl2fast v. 1.8.4
Reads were mapped against C.elegans genome assembly WBcel235 (ensembl release 84) using STAR v. 2.5.1b
strand specific readscounts per gene were calculated using  featureCounts (v. 1.4.6-p2, subread package)
differentially expressed genes were determined using DESeq2 (1.12.3)
Genome_build: WBcel235
Supplementary_files_format_and_content: readcounts per gene in tab separated value format

organism: Caenorhabditis elegans

source_name: Control (EV) treated day 15_whole worm

growth_protocol: Worms were grown in liquid culture as follows. NGM plus liquid media was prepared with 100µg/ml Ampicillin and EV HT115 bacteria re-suspended to a final density of 3x10^9 cells ml-1. Cell culture flasks with breathable filter caps were filled to the following capacity 75cm2 to a maximum of 50ml with a maximum density of 0.5 worms per µl per flask. Stock worms were washed from two 10cm2 NGM plates, sedimented and placed in a 100ml cell culture flask. All procedures from this point were carried out under a laminar flow hood to avoid contamination. Worm cultures were placed at 20°C in a shaking incubator at 40rpm and, once dense with egg producing adults, were then synchronised with NaOCl treatment followed by an over-night egg hatch in M9 buffer. L1 worms were counted and placed back into culture at the appropriate density. Worms were maintained in this manner for a minimum of three and a maximum of eight generations at optimal conditions. Adult worms were allowed to settle in 50ml falcon tubes at a 1:1 ratio to the density of the liquid culture. Sedimentation proceeded for 5-10 minutes depending on the age of the worm, adult worms sediment faster than larvae. The supernatant containing L1-L3 worms was removed by aspiration. Worms were re-suspended in NGM plus containing EV bacteria at a density of 1x10^9 cell ml-1. This was repeated six times. Worms were then carefully layered onto a 15ml column of 36% Percoll with NGM in a 50ml falcon. Worms were allowed to settle through the Percoll for 10 minutes and the top two thirds of the Percoll containing: dead worms, bagging worms, and egg clumps was aspirated. Worms were washed a further three times with NGM plus before being transferred into a fresh food culture. Percoll sedimentation was performed twice daily for the first five days and then once daily thereafter. A final sedimentation of in 40% Percoll was performed on days where samples were extracted.

extract_protocol:
Samples were flash frozen in Trizol regagent and RNA was extracted using standard protocols.
Libaries were prepared using Illumina's TruSeq stranded Total RNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031048 Rev. E). The ribozero steps of the protocol for rRNA depletion were carried out manually, while the following steps of library preparation were performed using the Bravo Automated Liquid Handling Platform (Agilent). Libraries were prepared from a starting amount of 500ng of total RNA and amplified in 11PCR cycles.

treatment_protocol: For knockdown conditions: worms were transferred to NGM plates with 100ug/ml ampicillin and 1mm IPTG on day 9 of adulthood. These plates were seeded with HT115 RNAi expressing bacteria containing plasmids targeting for EV(control), bec-1, pha-4, lgg-1 or atg-7. Samples for knockdown conditions were harvested three days later (day 12).

tag: genotype background

value: RNAi hypersensitive

value: Control (EV) treated

value: day 15


title: CXCR4+MET+CD44+ cells from ccRCC10


title: Non-cultured cells from ccRCC2


title: d15_ev_R3

description: Control (EV) treated day 15 replicate 3

tag: age


title: HepG2.2.15-shC2 cells, rep2

value: HepG2.2.15 cells

value: primary HCC cells

tag: treatment


title: d15_ev_R1

description: Control (EV) treated day 15 replicate 1


title: d9_ev_R4

description: Control (EV) treated day 9 replicate 4

source_name: Control (EV) treated day 9_whole worm

value: day 9


title: d9_ev_R1

description: Control (EV) treated day 9 replicate 1


title: d9_ev_R3

description: Control (EV) treated day 9 replicate 3


title: d6_ev_R4

description: Control (EV) treated day 6 replicate 4

source_name: Control (EV) treated day 6_whole worm

value: day 6


title: d18_ev_R3

description: Control (EV) treated day 18 replicate 3

source_name: Control (EV) treated day 18_whole worm

value: day 18


title: d18_ev_R1

description: Control (EV) treated day 18 replicate 1


title: d12_ev_R4_2

description: Control (EV) treated day 12 replicate 4

source_name: Control (EV) treated day 12_whole worm

value: day 12


title: d3_ev_R4

description: Control (EV) treated day 3 replicate 4

source_name: Control (EV) treated day 3_whole worm

value: day 3


title: d6_ev_R1

description: Control (EV) treated day 6 replicate 1


title: CXCR4+MET+CD44+ cells from ccRCC2

value: Male

value: clear cell renal cell cancer


title: d3_ev_R1

description: Control (EV) treated day 3 replicate 1


title: d18_ev_R4

description: Control (EV) treated day 18 replicate 4


title: d3_ev_R3

description: Control (EV) treated day 3 replicate 3


title: Acute Myeloid Leukemia Blast Side Population 1

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: gene expression data from hematopoietic side population

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: raw affymetrix data were normalized with Affymetrix console software

label: biotin

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Cells were sorted after a 3-day co-culture of peripheral blood AML blast sample at diagnosis with human medullar mesenchymal stromal cells.

extract_protocol: total RNA from cells were extracted with Rneasy Qiagen Extraction Kit by following manufacturer's instructions

treatment_protocol: sorted as main population or side population after hoechst 33342 treatment

value: side population AML blasts


title: Acute Myeloid Leukemia Blast Main Population 2

description: gene expression data from hematopoietic main population

value: main population AML blasts


title: d12_ev_R3

description: Control (EV) treated day 12 replicate 3


title: d6_ev_R3

description: Control (EV) treated day 6 replicate 3


title: Acute Myeloid Leukemia Blast Main Population 1


title: Acute Myeloid Leukemia Blast Side Population 2


title: Gpr151-KO::Chat-TRAP DW167 [1102]

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Immunopurified (IP)
polysome bound mRNA
1102_Gpr151-KO::Chat-TRAP DW167_CTTGTA_L005
1102

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 UCSC mm10 whole genome using STAR version 2.3.0e_r291, with default settings.
Quantification of aligned reads was done using htseq-count module, part of the ‘HTSeq’ framework, version 0.6.0, using default settings, with ‘union’ mode to handle reads overlapping more than one feature.
Differentially expressed genes were identified by performing a negative binomial test using DESeq2 (R-package version 1.4.5) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Counts text

source_name: 4 adult mice pooled

growth_protocol: All mice were maintained on a 12h light-dark cycle with ad lib access to food and water. Adult mice were used for all experiments (>8 weeks of age).

extract_protocol:
Brain regions of interest were microdissected, and homogenized immediately for IP using magnetic beads conjugated to anti-GFP. Total RNA was extracted from both the total homogenate (INPUT) and the IP fraction.
Ovation RNA-Seq System V2 kit (Nugen, Cat# 7102) was used with 10ug of RNA for MHb samples for generation of SPIA cDNA. 1ug of SPIA cDNA was fragmented to 250bp before proceeding with library prepartion using the TruSeq DNA Nano LT Sample Prep Kit (Illumina, Cat# 20015964).

treatment_protocol: Animals were sacrificed by live decapitation, brains were rapidly removed and regions of interest dissected on ice.

value: Medial Habenula

tag: transgene(s)

value: Gpr151-KO::Chat-TRAP DW167


title: Gpr151-KO::Chat-TRAP DW167 [1099]

description:
Immunopurified (IP)
polysome bound mRNA
1099_Gpr151-KO::Chat-TRAP DW167_ACAGTG_L007
1099


title: d12_ev_R1

description: Control (EV) treated day 12 replicate 1


title: Gpr151-KO::Chat-TRAP DW167 [1100]

description:
Immunopurified (IP)
polysome bound mRNA
1100_Gpr151-KO::Chat-TRAP DW167_ACAGTG_L002
1100


title: Chat-TRAP (DW167) [1093]

description:
Immunopurified (IP)
polysome bound mRNA
GSM4072460
1093

value: Chat-TRAP DW167


title: Gpr151-KO::Chat-TRAP DW167 [1101]

description:
Immunopurified (IP)
polysome bound mRNA
1101_Gpr151-KO::Chat-TRAP DW167__GCCAAT_L005
1101


title: Chat-TRAP (DW167) [1094]

description:
Immunopurified (IP)
polysome bound mRNA
GSM4072461
1094


title: Chat-TRAP (DW167) [1092]

description:
Immunopurified (IP)
polysome bound mRNA
GSM4072459
1092


title: Gpr151-KO::Chat-TRAP DW167 [855]

description:
Immunopurified (IP)
polysome bound mRNA
855_Gpr151-KO::Chat-TRAP DW167_CTTGTA_L008
855

source_name: 3 adult mice pooled


title: Chat-TRAP (DW167) [1091]

description:
Immunopurified (IP)
polysome bound mRNA
GSM4072458
1091


title: Gpr151-KO::Chat-TRAP DW167 [683]

description:
Immunopurified (IP)
polysome bound mRNA
683_Gpr151-KO::Chat-TRAP DW167_CTTGTA_L002
683


title: Chat-TRAP DW167 [682]

description:
Immunopurified (IP)
polysome bound mRNA
682_Chat_TRAP_DW167_GCCAAT_L002
682


title: Chat-TRAP (DW167) [852]

description:
Immunopurified (IP)
polysome bound mRNA
GSM4072446
852


title: Chat-TRAP (DW167) INPUT [824]

description:
Input
Total RNA
GSM4072443
824


title: T10G

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

description:
time point 10, pooled, replicate G
S66
genome Putnam et al. (2007)

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: whole-organism

growth_protocol: Animals were maintained as described in Hand et al. (1994) in the lab before deployment

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Adult Nematostella originally collected from Great Sippewissett Marsh, Massachusetts were maintained in the laboratory for several generations as described in Hand and Uhlinger (1992). In preparation for the study, salinity was adjusted to mimic field conditions (30 parts per thousand), and 200 anemones were transferred to marsh sediments of a tidally restricted pool in Sippewissett, MA (41°58’ N, 70°63’ W), where a native population of Nematostella is routinely collected (Hand and Uhlinger, 1994; Reitzel et al., 2013b) (Figure 1). To ensure recapture, anemones were housed in 10 small pens constructed from mesh netting and open plastic cages designed for rearing aquarium fish (Figure S1). Each pen was anchored into the sediment using steel tent stakes to ensure the pens would remain fully submerged at each tidal stage (Figure S1). On June 18, 2018, the pens were recovered hourly beginning at 0800, ZT = 3 and ending at 1700, ZT = 12. At each time point, 10 individuals from each pen were removed from the pens with a transfer pipette while still in the field and immediately placed in RNAlater. Four animals were prepared for sequencing as individuals (A, B, C, D) and the remaining six were pooled in groups of two (E, F, G) for each time point.

tag: timepoint

tag: sample type

value: pooled

tag: developmental stage

value: adult


title: MCF7_VEH_3

city: Richardson

first: Nikki

last: Delk

address: 800 West Campbell Road

institute: University of Texas at Dallas

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 3

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc/v0.11.2 and fastq_screen/v0.4.4
Reads were quality trimmed using fastq-mcf (ea-utils/v1.1.2-806).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes)
Duplicates were marked using picard-tools/v1.127
Read counts were generated using featureCounts (subread/v1.4.6).
Normalized read counts and differentially expressed genes found using edgeR/v3.2.4
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes raw read counts for each sample per gene

growth_protocol: MCF7 and MDA-MB-231 cells were grown in a 37°C, 5.0% (vol/vol) CO2 incubator in Dulbecco Modified Eagle Medium (DMEM; Gibco, Waltham, MA; 1185‐076) supplemented with 10% FB Essence (Seradigm, Radnor, PA; 3100‐500), 0.4mM of L‐glutamine (L‐glut; Gibco/Invitrogen, Waltham, MA; 25030081), and 10U/mL of penicillin G sodium and 10 mg/mL of streptomycin sulfate (pen‐strep; Gibco/Invitrogen; 15140122).

extract_protocol:
RNA was harvested using GeneJET RNA Purification Kit according to the manufacturer’s instructions (Thermo Scientific; K0732), RNA quantitiy and quality was then verified useng Biotek plate reader Gen 5 software, microspots protocol.
One microgram of total DNAse-treated RNA was prepared with DNAse 1, RNase-free(Thermo, #EN0521)

treatment_protocol: MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). MDA-MB-231 cells were treated with vehicle control (0.1% BSA in 1xPBS). At Day 5, total RNA was extracted for RNA-sequencing.

value: Breast

tag: genotype

value: cell line

tag: time

value: 5 days


title: MCF7_IL1A_2

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1a, 2

tag: tissue


title: X231_VEH_2

description:
MDA-MB-231 cells were treated with vehicle control (0.1% BSA in 1xPBS). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 2


title: MCF7_IL1B_3

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1β, 3


title: X231_VEH_1

description:
MDA-MB-231 cells were treated with vehicle control (0.1% BSA in 1xPBS). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 1


title: X231_VEH_3

description:
MDA-MB-231 cells were treated with vehicle control (0.1% BSA in 1xPBS). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 3


title: MCF7_IL1B_2

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1β, 2


title: MCF7_IL1A_3

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1a, 3


title: T10F

description:
time point 10, pooled, replicate F
S65
genome Putnam et al. (2007)


title: T10E

description:
time point 10, pooled, replicate E
S64
genome Putnam et al. (2007)


title: MCF7_VEH_2

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 2


title: MCF7_VEH_1

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
PBS (Vehicle control), 1


title: T10C

description:
time point 10, individual, replicate C
S62
genome Putnam et al. (2007)

value: individual


title: T10D

description:
time point 10, individual, replicate D
S63
genome Putnam et al. (2007)


title: T10A

description:
time point 10, individual, replicate A
S60
genome Putnam et al. (2007)


title: T10B

description:
time point 10, individual, replicate B
S61
genome Putnam et al. (2007)


title: T9G

description:
time point 9, pooled, replicate G
S59
genome Putnam et al. (2007)


title: T9F

description:
time point 9, pooled, replicate F
S58
genome Putnam et al. (2007)


title: WT_GLN_155

city: Boston

first: Rajesh

middle: K

last: Biswas

state: MA

address: 136 Harrison Avenue

department: Molecular Biology and Microbiology

institute: Tufts University Schoolof Medicine

description: paired-end

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts.
Reads were aligned to [NC_017544.1] using BWA and read counts were assigned to genes and other genomic features using custom scripts.
Differential expression analysis was conducted with DESeq2.
Genome_build: NC_017544.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Listeria monocytogenes 10403S

source_name: Cells in LDM containing glutamine

growth_protocol: Wild-type and ΔglnR strains were grown in LDM containing NH4 or glutamine as a principal nitrogen source. Overnight starter cultures grown at room temperature were inoculated in flasks containing respective media and allowed to grow at 37℃ in a shaking waterbath.

extract_protocol:
Cells stored in -80℃ were pelleted down, washed with cold TE buffer, and subjected to lysis by bead-beating in Trizol, followed by RNA isolation using a ZYMO kit.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol [Nature Methods, 12(4), 323–325]. Briefly, 500 ng-1 μg of total RNA was fragmented, depleted of genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described [Biotechniques. 2001 Apr;30(4):892-7]; (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform to generate paired end reads.

treatment_protocol: Cells were harvested at the logarithmic phase of growth at OD600=0.3 by mixing with an equal volume of cold ethanol:acetone (1:1) mixture and kept at -80℃.

tag: strain

value: WT


title: ΔglnR_GLN_156

description: paired-end

value: {delta}glnR


title: ΔglnR_GLN_152

description: paired-end


title: MCF7_IL1A_1

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1a, 1


title: MCF7_IL1B_1

description:
MCF7 cells were treated with vehicle control (0.1% BSA in 1xPBS), 25 ng/ml IL-1 alpha (Gold Biotechnology, 1110-01A-10), or 25 ng/ml IL-1 beta (Gold Biotechnology, 1110-01B-10). At Day 5, total RNA was extracted for RNA-sequencing.
25 ng/ml IL-1β, 1


title: WT_NH4_153

description: paired-end

source_name: Cells in LDM containing NH4


title: ΔglnR_NH4_150

description: paired-end


title: WT_NH4_149

description: paired-end


title: T9D

description:
time point 9, individual, replicate D
S56
genome Putnam et al. (2007)


title: T9C

description:
time point 9, individual, replicate C
S55
genome Putnam et al. (2007)


title: T9A

description:
time point 9, individual, replicate A
S53
genome Putnam et al. (2007)


title: T9B

description:
time point 9, individual, replicate B
S54
genome Putnam et al. (2007)


title: T8G

description:
time point 8, pooled, replicate G
S52
genome Putnam et al. (2007)


title: Normoxia_D11_2

city: Chengdu

first: Mingzhou

last: Li

address: huimin road No.211

institute: sichuan agricultural university

description:
Chinese Hamster
20_mRNA_tpm.xlsx/20_lncRNA_tpm.xlsx

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
To avoid artificial bias, we removed low-quality reads including those with ≥10% unidentified nucleotides, >10 nt aligned to the adapter with ≤10% mismatches allowed, and with >50% of bases with phred quality <5.
Clean data were mapped to the Cricetulus griseus reference genome (CriGri-PICR) using STAR (v.2.6.0c) with suggested parameters in GENCODE to identify mRNA transcripts
Then we performed a transcript's filtering and merging with software AssemblyLine (http://assemblyline.googlecode.com) and TACO (v.0.7.3).
transcripts with clipped exon (first or last exons <15 bp) or poorly assembled (transcript length ≤250 bp) were removed. Second, remaining transcripts were filtered from background noise, then subjected to taco_run (main function in TACO) for transcript's merging.
The transcripts annotated as PCG (protein coding genes) were discarded and remaining (putative non-coding) transcripts were used for the prediction of coding potential
putative non-coding transcripts sequences were translated in all six possible frames with Transeq (part of EMBOSS v.6.6.0) and count the significant domain hits against Pfam (release31) database with PfamScan (v.1.6) as well as coding sequence in reference genome.
Shared domains which hit by putative non-coding and coding sequence were considered to be likely with p>0.05 or odd<10 after fisher exact test, putatively non-coding transcripts that hit in likely domains were furtherly removed.
CPC2 (http://cpc2.cbi.pku.edu.cn/) was used to assess coding potential in both strands of the putatively non-coding sequences
Putative transcripts supported to be non-coding by PfamScan and CPC2 were considered to be lncRNAs.
The mRNA and lncRNA expression level of transcripts per kilobase million (TPM) of each sample was calculated by kallisto (v0.44.0)
Genome_build: CriGri-PICR
Supplementary_files_format_and_content: TPMs for mRNAs and lncRNAs

organism: Cricetulus griseus

source_name: Hamster Primary Preadipocyte isolated from iWAT

extract_protocol:
Total RNA was isolated from each cell sample using HiPure Total RNA Mini Kit (Magen, Guangzhou, China) according to the manufacturer’s instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: adipogenic differentiation for Day11

value: Primary Preadipocyte

value: iWAT

value: Normoxia


title: Hypoxia_D11_1

value: Hypoxia


title: Hypoxia_D11_2


title: ΔglnR_NH4_154

description: paired-end


title: Normoxia_D11_1


title: T8F

description:
time point 8, pooled, replicate F
S51
genome Putnam et al. (2007)


title: Hypoxia_D7_2

value: adipogenic differentiation for Day7


title: T9E

description:
time point 9, pooled, replicate E
S57
genome Putnam et al. (2007)


title: WT_GLN_151

description: paired-end


title: Hypoxia_D7_1


title: A549_cMYC

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
BWA alignment
MACS2 Peak-calling
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; ChIP-seq signal

source_name: Cancer cell line

extract_protocol:
Chromatin-IP
Following NEB ChIP-seq library preparation kit (E6200S)

tag: disease  state

value: Lung adenocarcinoma

tag: cell line

tag: chip antibody

value: cMYC (Cell Signaling #13987)


title: T8D

description:
time point 8, individual, replicate D
S49
genome Putnam et al. (2007)


title: T8E

description:
time point 8, pooled, replicate E
S50
genome Putnam et al. (2007)


title: Normoxia_D7_2


title: A549-MGAOE-MGA-A

value: MGA (Sigma #HPA042278)

value: Over-expressing MGA WT


title: T8C

description:
time point 8, individual, replicate C
S48
genome Putnam et al. (2007)

value: adult


title: A549-empty-MGA-B

value: Over-expressing Empty vector


title: Normoxia_D7_1


title: HCC adjacent normal tissue sample N2

city: Nanning

first: Xuefeng

last: Guo

state: Guangxi Zhuang Autonomous Region

address: 22 Shuangyong Road

department: 1.	Department of Epidemiology and Health Statistics

institute: Xuefeng Guo

description: Gene expression in  the hepatocellular carcinoma adjacent normal tissue sample N2

hyb_protocol: 1.0 ug of each labeled cRNA was mixed at 60°C for 30 minutes with a 25ul reaction, which inluded 10 × Blocking Agent  and 25 × Fragmentation Buffer. Then, 25ul 2 × GE Hybridization buffer was added to the mixture and hybridized to the LncRNA expression microarry for 17 hours at 65°C in an Agilent Hybridization Oven. At last, the hybridized microarry was washed 1 minutes with Gene expression  Wash Buffer 1 (Agilent) and 1 minutes with Gene expression Wash Buffer 2 (Agilent), then dried by brief centrifugation.

scan_protocol: After washing step, slides were immediately scanned with Agilent Microarray Scanner (G2505B) for one-color scan(Scan Region 61x 21.6 mm, Scan Resulution 5um, 5um Scanning mode is single pass, Dye channel is green and Green PMT is 100% ).

data_processing: The scanned images (.tif) were analyzed with Agilent Feature Extraction (FE) software (Version 11.0.1.1). Quantile normalization and subsequent data analysis were used with GeneSpring GX V12.1 software package (Agilent Technologies). Differential expression of LnRNAs and mRNAs in two groups were identified by P-value and FDR filtering.

source_name: Hepatocellular carcinoma adjacent normal tissue sample N2

label_protocol: Labeled cRNA was prepared from 1ug total RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442), and purified by Rneasy Mini Kit (Qiagen, 74104). The concentration and specific activity in cRNAs were measured by NanoDrop ND-1000.

extract_protocol: RNA for microarray chip was isolated with TRIzol Reagent (Invitrogen, USA) according to the manufacture's protocol.  The concentration and purity of RNA were tested with NanoDrop ND-1000 spectrophotometry (Thermo Scientific) and the integrity was measured by standard denaturing agarose gel.

treatment_protocol: HCC tissues and adjacent normal tissues were collected from the 5 HCC volunteers. All tissues collection was finished in 30 minutes and stored in liquid nitrogen until total RNA extraction.

value: HCC adjacent normal tissue

tag: gender

value: male


title: Hypoxia_D3_2

value: adipogenic differentiation for Day3

tag: cell type


title: RNA-seq_A549_siMYC_A

data_processing:
STAR alignment
RSEM normalization
quartile normalization
Genome_build: hg19
Supplementary_files_format_and_content: txt file; RSEM output (read counts) processed by quartile normalization

extract_protocol:
RNA was extracted using Qiagen RNeasy kit (74104) and mRNA was subsequently isolated using NEB poly(A) module (E7490)
Following NEB RNA-seq library preparation kit (E7420S)

value: siMYC (siRNA silencing MYC)


title: HCC adjacent normal tissue sample N5

description: Gene expression in  the hepatocellular carcinoma adjacent normal tissue sample N5

source_name: Hepatocellular carcinoma adjacent normal tissue sample N5


title: HCC adjacent normal tissue sample N1

description: Gene expression in  the hepatocellular carcinoma adjacent normal tissue sample N1

source_name: Hepatocellular carcinoma adjacent normal tissue sample N1


title: A549-empty-MGA-A


title: HCC tissue sample C3

description: Gene expression in  the hepatocellular carcinoma tissue sample C3

source_name: Hepatocellular carcinoma tissue sample C3

value: hepatocellular carcinoma (HCC) tissue


title: HCC adjacent normal tissue sample N3

description: Gene expression in  the hepatocellular carcinoma adjacent normal tissue sample N3

source_name: Hepatocellular carcinoma adjacent normal tissue sample N3


title: HCC adjacent normal tissue sample N4

description: Gene expression in  the hepatocellular carcinoma adjacent normal tissue sample N4

source_name: Hepatocellular carcinoma adjacent normal tissue sample N4

value: female


title: RNA-seq_A549_siMYC_B


title: T8A

description:
time point 8, individual, replicate A
S46
genome Putnam et al. (2007)

value: individual


title: HCC tissue sample C1

description: Gene expression in  the hepatocellular carcinoma tissue sample C1

source_name: Hepatocellular carcinoma tissue sample C1


title: HCC tissue sample C2

description: Gene expression in  the hepatocellular carcinoma tissue sample C2

source_name: Hepatocellular carcinoma tissue sample C2


title: RNA-seq_A549_siNC_B

value: siNC (siRNA negative control)


title: RNA-seq_A549_MGA_B

value: MGA (MGA overexpression vector)


title: RNA-seq_A549_siNC_A


title: HCC tissue sample C5

description: Gene expression in  the hepatocellular carcinoma tissue sample C5

source_name: Hepatocellular carcinoma tissue sample C5


title: T8B

description:
time point 8, individual, replicate B
S47
genome Putnam et al. (2007)


title: A549-MGAOE-MGA-B


title: T7F

description:
time point 7, pooled, replicate F
S44
genome Putnam et al. (2007)

value: pooled


title: RNA-seq_A549_Empty_B

value: Empty (empty vector)


title: T7G

description:
time point 7, pooled, replicate G
S45
genome Putnam et al. (2007)


title: RNA-seq_A549_Empty_A

value: Lung adenocarcinoma


title: A549_MGA_A

tag: antibody


title: A549_MGA_B


title: Normoxia_D3_1

description:
Chinese Hamster
20_mRNA_tpm.xlsx/20_lncRNA_tpm.xlsx

value: Primary Preadipocyte

value: iWAT

value: Normoxia


title: Hypoxia_D1_2

value: adipogenic differentiation for Day1

value: Hypoxia


title: T7D

description:
time point 7, individual, replicate D
S42
genome Putnam et al. (2007)

value: adult


title: T7E

description:
time point 7, pooled, replicate E
S43
genome Putnam et al. (2007)


title: Hypoxia_D3_1


title: Hypoxia_D1_1


title: Hypoxia_D0_1

value: adipogenic differentiation for Day0


title: Normoxia_D1_1


title: T6F

description:
time point 6, pooled, replicate F
S37
genome Putnam et al. (2007)


title: T6G

description:
time point 6, pooled, replicate G
S38
genome Putnam et al. (2007)


title: T7A

description:
time point 7, individual, replicate A
S39
genome Putnam et al. (2007)


title: Normoxia_D0_2


title: T7B

description:
time point 7, individual, replicate B
S40
genome Putnam et al. (2007)


title: T6E

description:
time point 6, pooled, replicate E
S36
genome Putnam et al. (2007)


title: T6D

description:
time point 6, individual, replicate D
S35
genome Putnam et al. (2007)


title: T6B

description:
time point 6, individual, replicate B
S33
genome Putnam et al. (2007)


title: T6A

description:
time point 6, individual, replicate A
S32
genome Putnam et al. (2007)


title: Normoxia_D0_1


title: T6C

description:
time point 6, individual, replicate C
S34
genome Putnam et al. (2007)


title: T5G

description:
time point 5, pooled, replicate G
S31
genome Putnam et al. (2007)


title: T5F

description:
time point 5, pooled, replicate F
S30
genome Putnam et al. (2007)


title: T5E

description:
time point 5, pooled, replicate E
S29
genome Putnam et al. (2007)


title: T7C

description:
time point 7, individual, replicate C
S41
genome Putnam et al. (2007)


title: T5A

description:
time point 5, individual, replicate A
S25
genome Putnam et al. (2007)


title: Normoxia_D1_2

description:
Chinese Hamster
20_mRNA_tpm.xlsx/20_lncRNA_tpm.xlsx


title: T4F

description:
time point 4, pooled, replicate F
S23
genome Putnam et al. (2007)


title: T4D

description:
time point 4, individual, replicate D
S22
genome Putnam et al. (2007)


title: Hypoxia_D0_2


title: Normoxia_D3_2

value: adipogenic differentiation for Day3


title: T5B

description:
time point 5, individual, replicate B
S26
genome Putnam et al. (2007)


title: T4G

description:
time point 4, pooled, replicate G
S24
genome Putnam et al. (2007)


title: T5D

description:
time point 5, individual, replicate D
S28
genome Putnam et al. (2007)


title: T4B

description:
time point 4, individual, replicate B
S20
genome Putnam et al. (2007)


title: HCC tissue sample C4

description: Gene expression in  the hepatocellular carcinoma tissue sample C4

source_name: Hepatocellular carcinoma tissue sample C4

tag: age


title: control-rep2-Input

city: Wuhan City

first: Qinglan

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
Trimmed reads were mapped to mouse reference genome (mm10) using BWA (version 0.7.15)
Data were filtered using the following specifications…
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: colon tissue

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Total DNA fragments were purified and then amplified to generate libraries using the VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604) and sequenced by Illumina Hiseq X Ten.

value: colon tissue

value: 7 week older


title: control-rep3-Input


title: control-rep1-Input


title: DSS-rep3-Input


title: T4A

description:
time point 4, individual, replicate A
S19
genome Putnam et al. (2007)


title: T3G

description:
time point 3, pooled, replicate G
S18
genome Putnam et al. (2007)


title: T3F

description:
time point 3, pooled, replicate F
S17
genome Putnam et al. (2007)


title: DSS-rep1-Input


title: control-rep3-H3K27ac


title: control-rep2-H3K27ac


title: DSS-rep2-Input


title: T3E

description:
time point 3, pooled, replicate E
S16
genome Putnam et al. (2007)


title: control-rep1-H3K27ac


title: DSS-rep3-H3K27ac


title: T4C

description:
time point 4, individual, replicate C
S21
genome Putnam et al. (2007)


title: DSS-rep2-H3K27ac


title: DSS-rep1-H3K27ac


title: T3C

description:
time point 3, individual, replicate C
S14
genome Putnam et al. (2007)


title: T3D

description:
time point 3, individual, replicate D
S15
genome Putnam et al. (2007)


title: T3B

description:
time point 3, individual, replicate B
S13
genome Putnam et al. (2007)


title: 8 3 dpf embryo neuronally expressing EWSR1-ERG

city: Leiden

first: Wietske

last: van der Ent

address: Einsteinweg 55

institute: Leiden University, Institute of Biology Leiden

data_processing:
GeneTiles was used for quantification and visualization of the RNAseq data
Bowtie2 is used to align the reads in the fastq file to the genome (obtained from Ensemble). Bowtie2 generates SAM files that contain the reads together with the location on the genome.
Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome, resulting in a sorted BAM file.
The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome, i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file.
Using the available annotation from Ensemble we can search the BAM file for reads within a gene (using exon starting positions and lengths). This is done with a python script. The output of this script is a tab separated file (tsv) containing the read counts per gene.
We used DESeq, an R-script to perform statistical analysis. The DESeq script is used to normalise the reads per gene, based on (divided by) the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P-value, by calculating the dispersion per gene using DESeq. The size factors as well as the P-values are stored in ‘tsv’ files.
Using a script, all tsv files are combined into tsv files , e.g. per experiment, chromosome, per filtered results of most significant reads or highest ratio between measurement and control.
Genome_build: Zv9_toplevel

organism: Danio rerio

source_name: Danio rerio embryo (Tg(14xUAS:GFP-EWSR1-ERG) x Et(E1b:Gal4-VP16)s1101t, Tg(UAS:Kaede) s1999t), 3 days post fertilization

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer (Next Advance, Averill Park, NY); subsequently RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions, and stored at -80°C. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Embryos with neuronally-expressed EWSR1-ERG

tag: biological replica


title: T3A

description:
time point 3, individual, replicate A
S12
genome Putnam et al. (2007)

source_name: whole-organism

tag: timepoint

value: individual


title: T5C

description:
time point 5, individual, replicate C
S27
genome Putnam et al. (2007)

tag: sample type


title: 7 3 dpf embryo neuronally expressing EWSR1-ERG


title: T2F

description:
time point 2, pooled, replicate F
S11
genome Putnam et al. (2007)

tag: developmental stage


title: 5 Wildtype sibling 3dpf


title: 4 Wildtype sibling 3dpf


title: 3 Wildtype sibling 3dpf


title: WT Tet1

city: Tianjin

first: Linlin

last: Liu

address: Weijin Road 97

institute: Nankai university

data_processing:
we analysed the raw data of fastq by Trim-galore, Bowtie2,samtools, deeptools  and MACS2 to get peaks.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data were included KO peaks and WT peaks got from MACS2 and we also offered bigwig files.

source_name: mouse testes spermatogonia cells

extract_protocol:
we use 20000 cells by FACS and incubate with Tet1-antibody.
DNA libraries were prepared for sequencing using standard  protocols.

value: spermatogonia cells

value: wild type


title: T1F

description:
time point 1, pooled, replicate F
S6
genome Putnam et al. (2007)

value: pooled


title: T1G

description:
time point 1, pooled, replicate G
S7
genome Putnam et al. (2007)


title: KO Tet1

value: Tet1 knock out


title: WT Input


title: KO Input


title: 6 3 dpf embryo neuronally expressing EWSR1-ERG


title: T1D

description:
time point 1, individual, replicate D
S4
genome Putnam et al. (2007)


title: T1E

description:
time point 1, pooled, replicate E
S5
genome Putnam et al. (2007)


title: T2C

description:
time point 2, individual, replicate C
S8
genome Putnam et al. (2007)


title: d14-1, dehydrated 4h, replicate 2

city: Hanoi

first: Kien

middle: Huu

last: Nguyen

state: Bac Tuliem

address: Pham Van Dong str., Bac Tuliem, Hanoi, Vietnam

department: Genetic Engineering Department

country: Viet Nam

institute: Agricultural Genetics Institute

description: Gene expression data from dehydrated kai2-2

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: d14-1, dehydrated 4h, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  µg RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and d14-1 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

value: rosette leaves

tag: time point

value: d14-1 mutant

value: 24 day-old

tag: condition

value: dehydrated


title: d14-1, dehydrated 4h, replicate 3

source_name: d14-1, dehydrated 4h, replicate 3

tag: tissue


title: d14-1, dehydrated 4h, replicate 1

source_name: d14-1, dehydrated 4h, replicate 1


title: T2D

description:
time point 2, pooled, replicate D
S9
genome Putnam et al. (2007)


title: d14-1, dehydrated 4h, replicate 4

source_name: d14-1, dehydrated 4h, replicate 4


title: T1B

description:
time point 1, individual, replicate B
S2
genome Putnam et al. (2007)


title: T1C

description:
time point 1, individual, replicate C
S3
genome Putnam et al. (2007)


title: T2E

description:
time point 2, pooled, replicate E
S10
genome Putnam et al. (2007)


title: d14-1, dehydrated 2h, replicate 2

source_name: d14-1, dehydrated 2h, replicate 2


title: d14-1, well-watered (0h), replicate 4

description: Gene expression data from well-watered kai2-2

source_name: d14-1, well-watered, replicate 4

value: well-watered


title: Spermatogonia cells, 11_monthsTet1KO_Rep3

data_processing:
we analyzed the raw data of fastq by Hisat2,samtools  and featurecounts to get the raw counts.
Genome_build: mm10
Supplementary_files_format_and_content: The reads counts of all 12 samples

extract_protocol:
we use 1000 cells by FACS and got cDNA library according to Smartseq2.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 11 months

tag: genotype


title: Spermatogonia cells, 11_months_WT_Rep3

value: WT


title: d14-1, dehydrated 2h, replicate 3

source_name: d14-1, dehydrated 2h, replicate 3


title: T1A

description:
time point 1, individual, replicate A
S1
genome Putnam et al. (2007)

value: adult


title: Spermatogonia cells, 11_monthsTet1KO_Rep2


title: d14-1, dehydrated 2h, replicate 1

source_name: d14-1, dehydrated 2h, replicate 1


title: Spermatogonia cells, 11_monthsWT_Rep2


title: d14-1, well-watered (0h), replicate 3

source_name: d14-1, well-watered, replicate 3


title: Spermatogonia cells, 11_months_Tet1KO_Rep1


title: d14-1, well-watered (0h), replicate 1

source_name: d14-1, well-watered, replicate 1


title: d14-1, well-watered (0h), replicate 2

source_name: d14-1, well-watered, replicate 2


title: Spermatogonia cells, 3_months_WT_Rep3

value: 3 months


title: Spermatogonia cells, 3_months_Tet1KO_Rep3


title: Spermatogonia cells, 11_months_WT_Rep1


title: Spermatogonia cells, 3_months_Tet1KO_Rep2


title: Spermatogonia cells, 3_months_WT_Rep2


title: Wildtype, dehydrated 4h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 2

value: Wildtype


title: Wildtype, dehydrated 4h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 3


title: Spermatogonia cells, 3_months_Tet1KO_Rep1


title: GNS166-DMSO-n2_(Clariom_S_Human)

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

country: Spain

institute: Biodonostia Research Institute

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: RMA normalized and Genes expressed differentially between each drug and DMSO were identified using Limma

label_protocol: standard affymetrix protocol

extract_protocol: Total RNA extraction was performed by Trizol (Life Technologies).

value: Glioblastoma cell line GNS179

tag: treatment

value: DMSO


title: GNS166-5uM-SAHA-n3_(Clariom_S_Human)

tag: cell line

value: SAHA


title: Wildtype, dehydrated 2h, replicate 3

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 3


title: Wildtype, dehydrated 4h, replicate 4

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 4


title: Spermatogonia cells, 3_months_WT_Rep1

value: spermatogonia cells


title: Wildtype, dehydrated 2h, replicate 4

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 4


title: Wildtype, dehydrated 2h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 1


title: Wildtype, well-watered (0h), replicate 4

description: Gene expression data from well-watered WT

source_name: WT, well-watered, replicate 4


title: GNS166-DMSO-n1_(Clariom_S_Human)


title: Wildtype, dehydrated 2h, replicate 2

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 2h, replicate 2


title: d14-1, dehydrated 2h, replicate 4

source_name: d14-1, dehydrated 2h, replicate 4


title: Wildtype, well-watered (0h), replicate 3

source_name: WT, well-watered, replicate 3


title: Wildtype, dehydrated 4h, replicate 1

description: Gene expression data from dehydrated WT

source_name: WT, dehydrated 4h, replicate 1


title: GNS166-DMSO-n3_(Clariom_S_Human)


title: Wildtype, well-watered (0h), replicate 2

source_name: WT, well-watered, replicate 2


title: Wildtype, well-watered (0h), replicate 1

source_name: WT, well-watered, replicate 1


title: GNS166-5uM-JOC1-n2_(Clariom_S_Human)


title: GNS166-5uM-SAHA-n2_(Clariom_S_Human)


title: RNA-seq_A549_MGA_A

source_name: Cancer cell line

value: Lung adenocarcinoma

value: MGA (MGA overexpression vector)


title: GNS166-5uM-SAHA-n1_(Clariom_S_Human)


title: GNS166-5uM-JOC1-n1_(Clariom_S_Human)


title: BC_12

status: Public on Jan 17 2020

city: Brussels

first: Sandra

last: Schmitz

address: Avenue Hippocrate, 54

department: Medical Oncology

country: Belgium

institute: Universite catholique de louvain

hyb_protocol: 250 ng of RNA was amplified and labeled using the Affymetrix  GeneChip® 3’ IVT Express Kit. RNA was hybridized  overnight to Affymetrix GeneChip HG-U133 Plus 2.0  (High Wycombe, UK), then stained and washed on an  Affymetrix Gene Chip® Fluidics Station 450.

scan_protocol: The array was then scanned to produce an image data file (DAT) and  a cell intensities data file (CEL).

data_processing: The dataset was normalized using the GCRMA method.

extract_protocol: Total RNA was extracted using the miRNeasy Mini  Kit from Qiagen (Venlo, Netherlands).

treatment_protocol: Cetuximab two weeks before surgery

tag: disease state

value: HNSCC

value: before treatment

tag: sample id

tag: tumor site

value: OC

tag: tumor loc

value: Tongue

tag: clinical staging

tag: tabac (uap)

tag: alcool (units)


title: BC_17


title: OC_15

value: after treatment


title: BC_15


title: OC_12


title: GNS166-5uM-JOC1-n3_(Clariom_S_Human)


title: BC_18


title: BC_10

value: L

value: epiglottis


title: BC_11

value: Floor of mouth


title: BC_14


title: BC_8


title: OC_8


title: BC_19


title: BC_9


title: BC_4


title: OC_9


title: OC_10


title: OC_14


title: BC_5

value: Internal cheek


title: OC_4


title: Corrected iPSC culture 2

city: Beijing

first: Guoxu

last: Song

address: No. 15, Datun Road, Chaoyang District, Beijing

institute: Institute of Biophysics, Chinese Academy of Science

description: Gene expression data from genetically corrected iPSCs

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned by using Affymetrix GeneChip Command Console (AGCC) that installed in GeneChip® Scanner 3000 7G.

data_processing: Data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings.

source_name: Corrected iPSC cultured cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Human iPSCs were cultured on Geltrex in Essential 8 medium.

extract_protocol: Total RNAs were purified from SCA3 iPSCs and genetically corrected iPSCs using Trizol (Invitrogen) according to the manufacture’s protocol (Affymetrix).

value: Corrected iPSC line 1A


title: Corrected iPSC culture 1


title: BC_7


title: OC_5


title: OC_6


title: OC_11


title: Csf2het replicate2

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Kallisto (v0.43.1) software was employed to determine the read count and transcripts per kilobase million (TPM) for each gene that was annotated in the GENCODE database (vM15). Genes  with an average TPM >1 were selected and then analyzed using the software DESeq2 to detect differentiall expressed genes at false discovery rate < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts in each sample

source_name: Isolated Tmem119+ microglia

extract_protocol:
Tmem119+ microglia were isolated by sorting directly into Qiagen RNeasy lysis buffer.The RNA was extracted the same day using a Rneasy Plus Micro Kit and stored at -80°C prior to processing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

tag: cell type

value: cerebral microglia

tag: age

value: 21 months old


title: Csf2het replicate1


title: SCA3 iPSC culture 2

description: Gene expression data from SCA3 iPSCs, before genetic correction.

source_name: SCA3 iPSC cultured cells

value: SCA3 patient-derived iPSC line CJJ-SCA3-iPS-C6


title: Csf2het replicate3


title: Csf1r_het replicate3


title: Csf1r_het replicate2

value: 24 months old


title: WT replicate2

value: wild type


title: OC_7


title: SCA3 iPSC culture 3


title: Dhet replicate1


title: BC_1


title: OC_13

value: passed


title: BC_2

value: alveolar ridge


title: Corrected iPSC culture 3


title: WT replicate1


title: BC_3

value: HNSCC


title: SCA3 iPSC culture 1


title: BC_16

value: before treatment


title: Eed_KO_Day16_Adult_ISC_scRNA

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

institute: Dana Farber Cancer Institute

data_processing:
ChIP-seq:bowtie2 version 2.3.4.3. For 150bp paired-end data, reads from the 'Read1' file were trimmed to 75bp and used for further analysis, RNA-seq: STAR aligner version 2.5.3a
ChIP-seq peak calling: SICER v0.0.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
scRNA-Seq – reads were processed using Cell Ranger v3.0.2
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
Supplementary_files_format_and_content: scRNA-Seq: raw gene-cell count matrix files

source_name: mouse intestinal villus cells

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C followed by digestion in TrypLE solution at 37°C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 5 consecutive days and every alternate day after that to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: B6;129 mixed background

value: Adult Epithelial cells; proximal 1/3 of intestine

value: Eed F/F; Lgr5EGFP-IRES-CreERT


title: LN229-U1

city: Jinan

first: Zhong

last: Yao

state: shandong province

address: No. 107 west Wenhua road

institute: Shandong University

data_processing:
raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing low quality reads and contaminating adaptor.
index of the reference genome was built using Bowtie v2.0.6 and clean reads were aligned to the reference genome using HISAT2
RPKM of each gene was calculated based on the length of gene and reads count mapped to this gene.
Genome_build: ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: treated with Ursodeoxycholic acid (UDCA)

growth_protocol: Cells were cultured at 37℃ in a humidified 5% CO2 atmosphere in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum, 1% penicillin and streptomycin.

extract_protocol:
six polyA mRNA-sequencing libriaries, including three from LN229 cells without treatment and three LN229 cells treated with UDCA were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with or without ursodeoxycholic 800uM for 48 hours

value: glioma

tag: tumor stage

value: grade IV glioma


title: LN229-U2


title: LN229-NC2

source_name: control


title: LN229-U3


title: Eed_KO_Day12_Adult_ISC_scRNA


title: OC_1

value: after treatment

value: OC

value: Tongue


title: OC_3


title: LN229-NC3


title: OC_2


title: Dhet replicate2

value: cerebral microglia


title: BC_13


title: Eed_KO_Day17 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day17 Adult ISC H3K27me3 ChIP Biological Replicate 1

source_name: mouse ISCs

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C followed by digestion in TrypLE solution at 37°C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with H3K27me3 antibody overnight (EMD Millipore 07-449) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

tag: antibody


title: WT replicate3

value: 21 months old


title: Eed_KO_Day7_Adult_ISC_scRNA


title: LN229-NC1

tag: tissue


title: Eed_KO_Day14 Adult ISC H3K27me3 ChIP Rep2

description: Eed_KO_Day14 Adult ISC H3K27me3 ChIP Biological Replicate 2

tag: strain


title: Eed_KO_Day14_Adult_ISC_RNA_Rep2

description:
Eed_KO_Day14_Adult_ISC_RNA Biological Replicate 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt

extract_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C followed by digestion in TrypLE solution at 37°C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were frozen in TRIzol reagent and stored at -80°C for subsequent RNA isolation.
Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 50 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

tag: genotype


title: Eed_KO_Day12 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day12 Adult ISC H3K27me3 ChIP Biological Replicate 1


title: Eed_KO_Day5 Adult ISC H3K27me3 ChIP Rep2

description: Eed_KO_Day5 Adult ISC H3K27me3 ChIP Biological Replicate 2


title: SW1573 4h

city: NY

first: Piro

last: Lito

address: 1275 York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequenced with Hiseq2500 Rapid Run in paired-end mode
Data was demultiplexed and analyzed using Cellranger 1.3.1 by using standard parameters.
Base-calling, alignment and abundance measurement was done with Cellranger as well.
The sequencing generated I1, R1, R2, R3 files, with read lengths of 8, 98, 14, and 10, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each cell line/time point the following files were generated: matrix.mtx is a sparse matrix file containg UMI count expression values; genes.tsv denotes the genes comprising the rows of the matrix; barcodes.tsv denotes the single-cells comprising the columns of the matrix.
Supplementary_files_format_and_content: logcounts.csv was generated by joining matrices from each time point/cell line followed by normalization and log transformation. cell.annotation.csv and gene.annotation.csv contain  annotations for rows and coumns of the log count matrix.

growth_protocol: DMEM 10% serum

extract_protocol:
Cells were collected and stored in cryopreservation medium at -80oC until experiment was completed. Viable single cell suspensions were subjected to scRNAseq exactly as described in protocol # CG00014 (10x Genomics).
Per manufacturer's recommendations for 3-prime v1 kits. Protocol # CD00026 (10x Genomics).
scRNA-seq

value: lung cancer cells

tag: ars1620 treatment


title: SW1573 0h

tag: cell line

value: Untreated


title: wt

city: Dresden

first: Jared

last: Sterneckert

state: Saxony

address: Fetscherstraße 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden

data_processing:
bcl2fastq: 2.17.1.14
alignment: Processed fastq files were aligned with the aligner GSNAP (v. 2014-12-17)  to the human reference hg38 from Ensembl with the support of splice site detection which was done with the Ensembl annotation (gtf file) version 81
genecount: Fragments were assigned to Gene with featureCounts (v1.4.6) and Ensembl annotation (gtf file) version 81 was used to find gene regions
Genome_build: hg38
Supplementary_files_format_and_content: bfx1300.genecounts.csv.gz is a tab separated file which is the featureCounts output. The first columns contain gene information such as Ensembl ID, Strand, Length, Start and End. Afterwards the 9 samples are listed

source_name: iPSC-derived neurons

growth_protocol: Neurons were cultured in N2B27 medium with 200 μM ascorbic acid, 10 ng/ml BDNF, and 20 ng/ml GDNF, 200 μM dbcAMP, 1 ng/ml TGFβ3

extract_protocol:
Total RNA was isolated using Qiagen RNeasy columns including a column DNase digest
mRNA was isolated from total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used 1: (Adaptor-Oligo 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligaton adapters were depleted by an XP bead purification (Beckman Coulter) adding bead in a ratio of 1:1. Indexing was done during the following PCR enrichment using custom amplification primers carring the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo_Seq AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T, primer2: GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T, primer3: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT. After two more XP beads purifications (1:1) libraries were quantified.

treatment_protocol: not applicable

value: untargetted control


title: Eed_KO_Day5 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day5 Adult ISC H3K27me3 ChIP Biological Replicate 1


title: wtKO

value: deletion in exon 2 to remove start codon


title: SW1573 72h


title: H2122 72h


title: SW1573 24h


title: E16 Hindgut RNA Biological Replicate 2

data_processing:
RNA-seq: STAR aligner, version 2.5.3a.
RNA-seq raw read counts: HTSeq
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression
Single Cell RNA: aligned with 10x CellRanger, version 3.0.2
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types

source_name: Mouse hindgut epithelial cells

extract_protocol:
Embryonic hindgut were digested in 0.25% Trypsin EDTA at 37°C for 30 minutes followed by neutralization with FBS. Epcam + cells were sorted by flow cytometry. Cells were immediately used for RNA extraction. Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
SMARTer-Seq v4 Ultra Low Input RNA Kit (Clontech) was used according to the manufacturer's instructions and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: 2mg tamoxifen on 1st and 2nd day and 1mg tamoxifen on 3rd day was intraperitoneally administered to knockout Ascl2. Diphtheria toxin (50 ug/kg) was intraperitoneally administered every other day 4 times to ablate stem cells

value: Embryonic epithelial cells from the hindgut

value: Wild-Type


title: E16 Hindgut RNA Biological Replicate 1


title: E14 Hindgut RNA Biological Replicate 2


title: H2122 0h


title: E12 Hindgut RNA Biological Replicate 2


title: H358 72h


title: E14 Hindgut RNA Biological Replicate 1


title: H2122 24h


title: E12 Hindgut RNA Biological Replicate 1


title: H358 24h


title: E11 Hindgut RNA Biological Replicate 2


title: E11 Hindgut RNA Biological Replicate 1


title: H358 4h


title: H358 0h


title: KO3

city: Vancouver

first: Pauline

last: Johnson

state: BC

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp × 42bp reads.
De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR, alignersm through Cufflinks Assembly.
Cuffdiff analysis was used for FPKM calculations as per Illumina basespace software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for the genes in all 6 samples. The columns WTBAL_FPKM & KOBAL_FPKM include the replicate averages.

source_name: Alveolar Macrophage

extract_protocol:
RNA extraction performed according to manufacturer's instructions using the Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were isolated from mice using bronchoalveolar lavage, using PBS and 2mM EDTA, then treated with RBC lysis buffer

tag: Sex

value: female

value: alveolar macrophage

value: 6-10 weeks


title: KO2


title: WT3


title: H2122 4h


title: WT2