title: Single Sert+ neuron 1387

description:
N8_SER57
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: AD, MTG sample 93--32

status: Public on Aug 01 2019

type: genomic

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

country: USA

institute: Arizona State University

description:
Alzheimer's MTG sample
MTG 93--32

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: iScan System according to user protocol

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: MTG sample 93--32

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: plate

tag: bead chip

tag: well position

tag: tissue

value: brain

tag: brain region

value: MTG

tag: gender

value: F

tag: age

tag: diagnosis

value: AD


title: Single Sert+ neuron 1376

type: SRA

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

description:
N4_SER63
Adult_DR_GEO_counts_cpm.txt

library_source: transcriptomic

data_processing:
Sequences from the NextSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were aligned to the mm10 genome using STAR version 2.6.1a (Dobin et al., 2013). Gene counts were produced using HTseq version 0.11.2 (Anders et al., 2015) with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’. Genes located on Y chromosome were removed from the count table to exclude sex bias.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for all Samples passing quality threshhold

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Lysis plates were prepared by dispensing 4 μl lysis buffer as described in (Tabula Muris et al., 2018). After dissociation, single tdTomato+ cells were sorted in 96-well plates using SH800S (Sony). Immediately after sorting, plates were sealed with a pre-labelled aluminum seal, centrifuged, and flash frozen on dry ice. cDNA synthesis and library preparation were performed using the Smart-seq2 protocol (Picelli et al., 2014). Wells of each library plate were pooled using a Mosquito liquid handler (TTP Labtech). Pooling was followed by two purifications using 0.7x AMPure beads (Fisher, A63881). Library quality was assessed using capillary electrophoresis on a Fragment Analyzer (AATI), and libraries were quantified by qPCR (Kapa Biosystems, KK4923) on a CFX96 Touch Real-Time PCR Detection System (Bio-Rad). Libraries were sequenced on the NextSeq 500 Sequencing System (Illumina) using 2 × 75-bp paired-end reads and 2 × 8-bp index reads.
Smrt-seq2

tag: strain

value: Sert+ neurons

value: 40–45 days

value: All DR

tag: genotype

value: Sert-tdTomato-Cre cross with Ai14


title: AD, MTG sample 97--44

description:
Alzheimer's MTG sample
MTG 97--44

source_name: MTG sample 97--44

value: M


title: AD, MTG sample 97--20

description:
Alzheimer's MTG sample
MTG 97--20

source_name: MTG sample 97--20


title: Single Sert+ neuron 1373

description:
N3_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--27

description:
Alzheimer's MTG sample
MTG 97--27

source_name: MTG sample 97--27


title: AD, MTG sample 97--48

description:
Alzheimer's MTG sample
MTG 97--48

source_name: MTG sample 97--48


title: AD, MTG sample 04--44

description:
Alzheimer's MTG sample
MTG 04--44

source_name: MTG sample 04--44


title: Single Sert+ neuron 1371

description:
N24_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--33

description:
Alzheimer's MTG sample
MTG 97--33

source_name: MTG sample 97--33


title: Single Sert+ neuron 1370

description:
N24_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1374

description:
N3_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1375

description:
N4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1369

description:
N24_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 95--33

description:
Alzheimer's MTG sample
MTG 95--33

source_name: MTG sample 95--33


title: AD, MTG sample 05--35

description:
Alzheimer's MTG sample
MTG 05--35

source_name: MTG sample 05--35


title: Single Sert+ neuron 1372

description:
N3_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 06--48

description:
Alzheimer's MTG sample
MTG 06--48

source_name: MTG sample 06--48


title: AD, MTG sample 04--28

description:
Alzheimer's MTG sample
MTG 04--28

source_name: MTG sample 04--28


title: AD, MTG sample 07--06

description:
Alzheimer's MTG sample
MTG 07--06

source_name: MTG sample 07--06


title: Single Sert+ neuron 1365

description:
N22_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1367

description:
N23_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1368

description:
N23_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 01--15

description:
Alzheimer's MTG sample
MTG 01--15

source_name: MTG sample 01--15


title: Single Sert+ neuron 1364

description:
N22_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 05--19

description:
Alzheimer's MTG sample
MTG 05--19

source_name: MTG sample 05--19


title: Single Sert+ neuron 1378

description:
N5_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1363

description:
N22_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--52

description:
Alzheimer's MTG sample
MTG 99--52

source_name: MTG sample 99--52


title: Single Sert+ neuron 1362

description:
N21_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1366

description:
N23_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 01--11

description:
Alzheimer's MTG sample
MTG 01--11

source_name: MTG sample 01--11


title: AD, MTG sample 01--18

description:
Alzheimer's MTG sample
MTG 01--18

source_name: MTG sample 01--18


title: Single Sert+ neuron 1361

description:
N21_SER60
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1360

description:
N21_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--38

description:
Alzheimer's MTG sample
MTG 03--38

source_name: MTG sample 03--38


title: AD, MTG sample 01--28

description:
Alzheimer's MTG sample
MTG 01--28

source_name: MTG sample 01--28


title: AD, MTG sample 00--35

description:
Alzheimer's MTG sample
MTG 00--35

source_name: MTG sample 00--35


title: AD, MTG sample 01--34

description:
Alzheimer's MTG sample
MTG 01--34

source_name: MTG sample 01--34


title: AD, MTG sample 01--13

description:
Alzheimer's MTG sample
MTG 01--13

source_name: MTG sample 01--13


title: AD, MTG sample 07--15

description:
Alzheimer's MTG sample
MTG 07--15

source_name: MTG sample 07--15


title: Single Sert+ neuron 1357

description:
N20_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1353

description:
N19_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 00--18

description:
Alzheimer's MTG sample
MTG 00--18

source_name: MTG sample 00--18


title: Single Sert+ neuron 1356

description:
N2_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1358

description:
N20_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1352

description:
N19_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1359

description:
N20_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1355

description:
N2_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1354

description:
N2_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 08--69

description:
Alzheimer's MTG sample
MTG 08--69

source_name: MTG sample 08--69


title: AD, MTG sample 07--57

description:
Alzheimer's MTG sample
MTG 07--57

source_name: MTG sample 07--57


title: AD, MTG sample 07--20

description:
Alzheimer's MTG sample
MTG 07--20

source_name: MTG sample 07--20


title: Single Sert+ neuron 1350

description:
N18_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1349

description:
N18_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--50

description:
Alzheimer's MTG sample
MTG 07--50

source_name: MTG sample 07--50


title: AD, MTG sample 07--17

description:
Alzheimer's MTG sample
MTG 07--17

source_name: MTG sample 07--17


title: AD, MTG sample 03--02

description:
Alzheimer's MTG sample
MTG 03--02

source_name: MTG sample 03--02


title: Single Sert+ neuron 1348

description:
N18_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--07

description:
Alzheimer's MTG sample
MTG 03--07

source_name: MTG sample 03--07


title: Single Sert+ neuron 1346

description:
N17_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 01--45

description:
Alzheimer's MTG sample
MTG 01--45

source_name: MTG sample 01--45


title: AD, MTG sample 98--14

description:
Alzheimer's MTG sample
MTG 98--14

source_name: MTG sample 98--14


title: AD, MTG sample 02--28

description:
Alzheimer's MTG sample
MTG 02--28

source_name: MTG sample 02--28


title: Single Sert+ neuron 1347

description:
N17_SER64
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: AD, MTG sample 96--50

description:
Alzheimer's MTG sample
MTG 96--50

source_name: MTG sample 96--50


title: Single Sert+ neuron 1340

description:
N15_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--18

description:
Alzheimer's MTG sample
MTG 97--18

source_name: MTG sample 97--18


title: Single Sert+ neuron 1345

description:
N17_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1351

description:
N19_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1342

description:
N16_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--25

description:
Alzheimer's MTG sample
MTG 97--25

source_name: MTG sample 97--25


title: AD, MTG sample 94--20

description:
Alzheimer's MTG sample
MTG 94--20

source_name: MTG sample 94--20


title: AD, MTG sample 97--07

description:
Alzheimer's MTG sample
MTG 97--07

source_name: MTG sample 97--07


title: AD, MTG sample 97--16

description:
Alzheimer's MTG sample
MTG 97--16

source_name: MTG sample 97--16


title: Single Sert+ neuron 1336

description:
N14_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1339

description:
N15_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1343

description:
N16_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1337

description:
N14_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--26

description:
Alzheimer's MTG sample
MTG 97--26

source_name: MTG sample 97--26


title: Single Sert+ neuron 1338

description:
N14_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1335

description:
N13_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 05--05

description:
Alzheimer's MTG sample
MTG 05--05

source_name: MTG sample 05--05


title: Single Sert+ neuron 1334

description:
N13_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--54

description:
Alzheimer's MTG sample
MTG 03--54

source_name: MTG sample 03--54


title: AD, MTG sample 96--31

description:
Alzheimer's MTG sample
MTG 96--31

source_name: MTG sample 96--31


title: AD, MTG sample 07--02

description:
Alzheimer's MTG sample
MTG 07--02

source_name: MTG sample 07--02


title: Single Sert+ neuron 1333

description:
N13_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1344

description:
N16_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 98--17

description:
Alzheimer's MTG sample
MTG 98--17

source_name: MTG sample 98--17


title: Single Sert+ neuron 1332

description:
N12_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 00--33

description:
Alzheimer's MTG sample
MTG 00--33

source_name: MTG sample 00--33


title: Single Sert+ neuron 1330

description:
N12_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1329

description:
N11_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 00--12

description:
Alzheimer's MTG sample
MTG 00--12

source_name: MTG sample 00--12


title: AD, MTG sample 06--58

description:
Alzheimer's MTG sample
MTG 06--58

source_name: MTG sample 06--58


title: Single Sert+ neuron 1328

description:
N11_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1327

description:
N11_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1326

description:
N10_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--33

description:
Alzheimer's MTG sample
MTG 99--33

source_name: MTG sample 99--33


title: AD, MTG sample 00--10

description:
Alzheimer's MTG sample
MTG 00--10

source_name: MTG sample 00--10


title: AD, MTG sample 99--56

description:
Alzheimer's MTG sample
MTG 99--56

source_name: MTG sample 99--56


title: Single Sert+ neuron 1331

description:
N12_SER63
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1325

description:
N10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1341

description:
N15_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 02--07

description:
Alzheimer's MTG sample
MTG 02--07

source_name: MTG sample 02--07


title: Single Sert+ neuron 1324

description:
N10_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--14

description:
Alzheimer's MTG sample
MTG 03--14

source_name: MTG sample 03--14


title: Single Sert+ neuron 1323

description:
N1_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 01--43

description:
Alzheimer's MTG sample
MTG 01--43

source_name: MTG sample 01--43


title: AD, MTG sample 05--25

description:
Alzheimer's MTG sample
MTG 05--25

source_name: MTG sample 05--25


title: AD, MTG sample 02--22

description:
Alzheimer's MTG sample
MTG 02--22

source_name: MTG sample 02--22


title: Single Sert+ neuron 1322

description:
N1_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--42

description:
Alzheimer's MTG sample
MTG 07--42

source_name: MTG sample 07--42


title: Single Sert+ neuron 1397

description:
O10_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1320

description:
M9_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1318

description:
M9_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--69

description:
Alzheimer's MTG sample
MTG 07--69

source_name: MTG sample 07--69


title: AD, MTG sample 07--54

description:
Alzheimer's MTG sample
MTG 07--54

source_name: MTG sample 07--54


title: Single Sert+ neuron 1317

description:
M8_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 06--60

description:
Alzheimer's MTG sample
MTG 06--60

source_name: MTG sample 06--60


title: Single Sert+ neuron 1316

description:
M8_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 03--30

description:
Alzheimer's MTG sample
MTG 03--30

source_name: MTG sample 03--30


title: AD, MTG sample 08--45

description:
Alzheimer's MTG sample
MTG 08--45

source_name: MTG sample 08--45


title: Single Sert+ neuron 1312

description:
M7_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 95--10

description:
Alzheimer's MTG sample
MTG 95--10

source_name: MTG sample 95--10


title: Single Sert+ neuron 1314

description:
M7_SER64
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1311

description:
M6_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1315

description:
M8_SER57
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 97--15

description:
Alzheimer's MTG sample
MTG 97--15

source_name: MTG sample 97--15


title: Single Sert+ neuron 1310

description:
M6_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 98--07

description:
Alzheimer's MTG sample
MTG 98--07

source_name: MTG sample 98--07


title: Single Sert+ neuron 1321

description:
N1_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 04--66

description:
Alzheimer's MTG sample
MTG 04--66

source_name: MTG sample 04--66


title: AD, MTG sample 96--17

description:
Alzheimer's MTG sample
MTG 96--17

source_name: MTG sample 96--17


title: Single Sert+ neuron 1309

description:
M6_SER57
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1308

description:
M5_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--08

description:
Alzheimer's MTG sample
MTG 07--08

source_name: MTG sample 07--08


title: AD, MTG sample 06--54

description:
Alzheimer's MTG sample
MTG 06--54

source_name: MTG sample 06--54


title: AD, MTG sample 06--30

description:
Alzheimer's MTG sample
MTG 06--30

source_name: MTG sample 06--30


title: Single Sert+ neuron 1307

description:
M5_SER60
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1306

description:
M5_SER56
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 08--41

description:
Alzheimer's MTG sample
MTG 08--41

source_name: MTG sample 08--41


title: Single Sert+ neuron 1319

description:
M9_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 05--58

description:
Alzheimer's MTG sample
MTG 05--58

source_name: MTG sample 05--58


title: AD, MTG sample 06--26

description:
Alzheimer's MTG sample
MTG 06--26

source_name: MTG sample 06--26


title: Single Sert+ neuron 1305

description:
M4_SER67
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1304

description:
M4_SER63
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1313

description:
M7_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--07

description:
Alzheimer's MTG sample
MTG 99--07

source_name: MTG sample 99--07


title: Single Sert+ neuron 1302

description:
M3_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--10

description:
Alzheimer's MTG sample
MTG 99--10

source_name: MTG sample 99--10


title: Single Sert+ neuron 1303

description:
M4_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1300

description:
M3_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1299

description:
M24_SER67
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--39

description:
Alzheimer's MTG sample
MTG 99--39

source_name: MTG sample 99--39


title: AD, MTG sample 99--28

description:
Alzheimer's MTG sample
MTG 99--28

source_name: MTG sample 99--28


title: AD, MTG sample 00--11

description:
Alzheimer's MTG sample
MTG 00--11

source_name: MTG sample 00--11


title: AD, MTG sample 00--50

description:
Alzheimer's MTG sample
MTG 00--50

source_name: MTG sample 00--50


title: Single Sert+ neuron 1298

description:
M24_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 99--60

description:
Alzheimer's MTG sample
MTG 99--60

source_name: MTG sample 99--60


title: Single Sert+ neuron 1296

description:
M23_SER64
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 02--29

description:
Alzheimer's MTG sample
MTG 02--29

source_name: MTG sample 02--29


title: AD, MTG sample 08--01

description:
Alzheimer's MTG sample
MTG 08--01

source_name: MTG sample 08--01


title: Single Sert+ neuron 1297

description:
M24_SER57
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1294

description:
M23_SER56
Adult_DR_GEO_counts_cpm.txt


title: Single Sert+ neuron 1295

description:
M23_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 02--41

description:
Alzheimer's MTG sample
MTG 02--41

source_name: MTG sample 02--41


title: Single Sert+ neuron 1293

description:
M22_SER67
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons


title: Single Sert+ neuron 1292

description:
M22_SER63
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 07--29

description:
Alzheimer's MTG sample
MTG 07--29

source_name: MTG sample 07--29


title: AD, MTG sample 08--59

description:
Alzheimer's MTG sample
MTG 08--59

source_name: MTG sample 08--59


title: AD, MTG sample 07--09

description:
Alzheimer's MTG sample
MTG 07--09

source_name: MTG sample 07--09


title: AD, MTG sample 96--09

description:
Alzheimer's MTG sample
MTG 96--09

source_name: MTG sample 96--09


title: Single Sert+ neuron 1291

description:
M22_SER57
Adult_DR_GEO_counts_cpm.txt


title: H3K9ac.ACSS2_KD.Untreated.R3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
07232018_H3K9ac.KD.Untreated.bw
H3K9ac-Input.KD.Untreated_peaks.FDR_0.001.bed

library_source: genomic

data_processing:
Alignment: chIP-seq tags generated with the NextSeq 500 platform were demultiplexed with the bcl2fastq utility and aligned to the mouse reference genome (assembly  GRCm38/mm10) using STAR v2.5.2a with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999
Tracks: aligned tags were pooled across replicates and tracks were generated using BEDtools genomeCoverageBed -bg, then the resulting bedGraphs were adjusted for library size by multiplying tag counts by the RPM coefficient and subtracting a similarly adjusted input track. BedGraphs were then converted to bigWig using the UCSC Genome Browser tool bedGraphToBigWig.
Peaks: aligned tags were pooled across replicates and peaks were called using MACS2 callpeak (with matched input as a control) and peaks were filtered with a q-value of 0.001 or lower to correct for the multiple hypothesis testing problem
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs are track files and BED files are peak files

source_name: hippocampus

growth_protocol: Male mice were aged to 8 weeks

extract_protocol:
ChIP-seq was performed as previously described (Nativio et al, Nat Neuroscience 2018) with modifications for mouse brain preparation. Briefly, ~20 mg dorsal hippocampus from each mouse was minced on ice and crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min. Nuclei were prepared by dounce homogenization of crosslinked tissue in nuclei isolation buffer (50 mM Tris-HCl at pH 7.5, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose) with freshly added protease inhibitors and sodium butyrate. Nuclei were lysed in nuclei lysis buffer (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with freshly added protease inhibitors and sodium butyrate and chromatin was sheared using a Covaris S220 sonicator to ~250 bp size. Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction with 5 ul H3K9ac antibody (Active Motif, cat # 39137; lot # 09811002 ) or 4 ul H3K27ac antibody (Abcam, cat #4729; lot # GR323132-1 (Piazza et al, Nat Commun 2018)) preconjugated to Protein G Dynabeads (Life Technologies). 10% of the chromatin was saved as Input. ChIP reactions were incubated overnight at 4°C with rotation and washed three times in wash buffer. Immunoprecipitated DNA was eluted from the beads, reversed crosslinked and purified together with Input DNA.
10 ng DNA (either ChIP or Input) was used to construct sequencing libraries using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-ended sequenced (75 bp) on the NextSeq 500 platform (Illumina) in accordance with the manufacturer’s protocol.

treatment_protocol: EtOH injection: ethanol was administered via intraperitoneal injection and dosed at 2 g/kg (20% solution in saline, filtered through a Stericup GV filter). ACSS2 shRNA: adult mice (8+ weeks of age) were anaesthetized with isoflurane gas (1–5% to maintain surgical plane) and placed in a sterile field within a stereotaxic device. Artificial tears were applied to eyes to ensure sufficient lubrication. Animals received an injection of bupivacaine (2.5 mg kg−1) for local anaesthesia before the skin was disinfected with betadine solution and the skull exposed with a short incision using sterile surgical equipment. A small hole (about 0.5 mm) was drilled in the skull over the target area using a stereotax and a stereotactic drill. A micro-syringe filled with viral vector was inserted into the dorsal hippocampus and slowly removed following injection (AP, − 2.0 mm; DV, − 1.4 mm; ML, ± 1.5 mm from bregma). ACSS2 knockdown vector, AAV2/9; U6.shACSS2.CMV.EGFP. All animals received a single dose of subcutaneous meloxicam (5 mg kg) as analgesia at induction and one dose per day for two days postoperatively as needed.

value: hippocampus

tag: chip antibody

value: H3K9ac (Active Motif, cat # 39137; lot # 09811002)

value: ACSS2 KD

tag: treatment


title: Single Sert+ neuron 1301

description:
M3_SER60
Adult_DR_GEO_counts_cpm.txt


title: AD, MTG sample 95--15

description:
Alzheimer's MTG sample
MTG 95--15

source_name: MTG sample 95--15


title: AD, MTG sample 99--06

description:
Alzheimer's MTG sample
MTG 99--06

source_name: MTG sample 99--06


title: AD, MTG sample 05--57

description:
Alzheimer's MTG sample
MTG 05--57

source_name: MTG sample 05--57


title: H3K9ac.ACSS2_KD.Untreated.R2


title: AD, MTG sample 03--59

description:
Alzheimer's MTG sample
MTG 03--59

source_name: MTG sample 03--59


title: AD, MTG sample 96--41

description:
Alzheimer's MTG sample
MTG 96--41

source_name: MTG sample 96--41


title: H3K9ac.ACSS2_KD.Untreated.R1


title: AD, MTG sample 06--12

description:
Alzheimer's MTG sample
MTG 06--12

source_name: MTG sample 06--12


title: H3K9ac.Control.EtOH.R2

description:
07232018_H3K9ac.WT.EtOH.bw
H3K9ac-Input.WT.EtOH_peaks.FDR_0.001.bed

value: Control

value: EtOH


title: H3K9ac.Control.EtOH.R1


title: H3K9ac.Control.Untreated.R2

description:
07232018_H3K9ac.WT.Untreated.bw
H3K9ac-Input.WT.Untreated_peaks.FDR_0.001.bed


title: H3K9ac.Control.Untreated.R1


title: RNA.ACSS2i.Acetate.R4

description: Counts Table - Acetate.txt

data_processing:
Alignment: data were aligned to mouse assembly mm10 using STAR v2.5.2a with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: tags were counted over exons to give gene-level tag counts with HTSeq v0.6.1p1 with parameters -f sam -r pos -s reverse -t exon -i gene_id
Differential Expression: tag counts were loaded into R and processed using DESeq2 with a design model ~Treatment+Inhibitor+Treatment:Inhibitor
Genome_build: mm10
Supplementary_files_format_and_content: Tag counts per gene per HTSeq are provided as a text table

molecule: total RNA

source_name: hippocampus neurons

growth_protocol: Plated primary hippocampal neurons were obtained from the Neurons R Us neuronal core at the University of Pennsylvania. Cells were maintained in neurobasal medium (NBM; Gibco) supplemented with GlutaMAX (Gibco) and B27 (Gibco).

extract_protocol:
Cells were lyzed using QIAzol (Qiagen) and RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNAseq libraries were prepared using the NEBNext Ultra II Directional RNA library prep kit (NEB).

treatment_protocol: After 7 days of differentiation, cells were treated for 24 hours with 5 mM acetate or vehicle (NBM) in the presence or absence of 20uM ACSS2 inhibitor or vehicle (DMSO diluted into NBM).

tag: cell type

value: hippocampus neurons

tag: inhibitor

value: ACSS2 Inhibitor

value: Acetate


title: AD, MTG sample 01--04

description:
Alzheimer's MTG sample
MTG 01--04

source_name: MTG sample 01--04

value: brain


title: AD, MTG sample 99--43

description:
Alzheimer's MTG sample
MTG 99--43

source_name: MTG sample 99--43

value: MTG


title: AD, MTG sample 00--37

description:
Alzheimer's MTG sample
MTG 00--37

source_name: MTG sample 00--37


title: AD, MTG sample 01--09

description:
Alzheimer's MTG sample
MTG 01--09

source_name: MTG sample 01--09

value: F


title: AD, MTG sample 99--64

description:
Alzheimer's MTG sample
MTG 99--64

source_name: MTG sample 99--64

value: AD


title: RNA.ACSS2i.Acetate.R3

description: Counts Table - Acetate.txt


title: Single Sert+ neuron 1290

description:
M21_SER64
Adult_DR_GEO_counts_cpm.txt

source_name: Sert+ neurons

value: Sert+ neurons


title: RNA.ACSS2i.Acetate.R2

description: Counts Table - Acetate.txt


title: AD, MTG sample 03--36

description:
Alzheimer's MTG sample
MTG 03--36

source_name: MTG sample 03--36


title: AD, MTG sample 07--27

description:
Alzheimer's MTG sample
MTG 07--27

source_name: MTG sample 07--27


title: RNA.ACSS2i.Acetate.R1

description: Counts Table - Acetate.txt


title: RNA.ACSS2i.Untreated.R3

description: Counts Table - Acetate.txt

value: Vehicle


title: AD, MTG sample 08--82

description:
Alzheimer's MTG sample
MTG 08--82

source_name: MTG sample 08--82


title: H3K9ac.Control.EtOH.R3

source_name: hippocampus


title: AD, MTG sample 06--09

description:
Alzheimer's MTG sample
MTG 06--09

source_name: MTG sample 06--09


title: RNA.ACSS2i.Untreated.R2

description: Counts Table - Acetate.txt


title: AD, MTG sample 01--53

description:
Alzheimer's MTG sample
MTG 01--53

source_name: MTG sample 01--53


title: RNA.ACSS2i.Untreated.R1

description: Counts Table - Acetate.txt


title: H3K9ac.Control.Untreated.R3


title: AD, MTG sample 03--21

description:
Alzheimer's MTG sample
MTG 03--21

source_name: MTG sample 03--21


title: AD, MTG sample 03--05

description:
Alzheimer's MTG sample
MTG 03--05

source_name: MTG sample 03--05


title: RNA.DMSO.Acetate.R3

description: Counts Table - Acetate.txt

value: DMSO


title: AD, MTG sample 04--47

description:
Alzheimer's MTG sample
MTG 04--47

source_name: MTG sample 04--47


title: RNA.DMSO.Acetate.R1

description: Counts Table - Acetate.txt


title: AD, MTG sample 03--03

description:
Alzheimer's MTG sample
MTG 03--03

source_name: MTG sample 03--03


title: RNA.DMSO.Acetate.R2

description: Counts Table - Acetate.txt

source_name: hippocampus neurons


title: RNA.DMSO.Acetate.R4

description: Counts Table - Acetate.txt


title: AD, MTG sample 97--29

description:
Alzheimer's MTG sample
MTG 97--29

source_name: MTG sample 97--29


title: AD, MTG sample 96--46

description:
Alzheimer's MTG sample
MTG 96--46

source_name: MTG sample 96--46


title: RNA.DMSO.Untreated.R2

description: Counts Table - Acetate.txt


title: AD, MTG sample 06--11

description:
Alzheimer's MTG sample
MTG 06--11

source_name: MTG sample 06--11


title: RNA.DMSO.Untreated.R4

description: Counts Table - Acetate.txt


title: AD, MTG sample 04--29

description:
Alzheimer's MTG sample
MTG 04--29

source_name: MTG sample 04--29


title: RNA.DMSO.Untreated.R1

description: Counts Table - Acetate.txt


title: AD, MTG sample 03--40

description:
Alzheimer's MTG sample
MTG 03--40

source_name: MTG sample 03--40


title: 6-month-2

city: Jerusalem

first: Jacob

last: Rachmilewitz

address: Ein -Kerem

country: Israel

institute: Hadassah Hebrew University medical center

data_processing:
Raw fastq files were quality-trimmed at the 3' end with a threshold of 25.
Processed fastq files were mapped to the mouse genome with up to 5 mismatches, using tophat (v2.0.11).
Counting, normalization and differential expression were calculated using Cufflinks (v2.2.1), with the bias correction parameter and a threshold of at least 3 counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file which contains the results of the Cuffdiff run as is (the gene_exp.diff file), preceded by general gene details (taken from the results of a BioMart query).

source_name: Liver

growth_protocol: Mice were purchased from Harlan were grown under SPF condtions until sacrifies

extract_protocol:
Total RNA was isolated from liver samples using Trizol reagent (Life Technologies, Paisley, UK) and purified using MaXtract High Density (QIAGEN, Redwood City, CA). RNA yield and quantity was determined using a Nanodrop spectrophotometer ND-1000 (Thermo scientific, Wilmington, DE). The RNA quality was tested using a ND-1000 V3.7.1, according to the manufacturer’s instructions and assigned an RNA integrity number (RIN). Only samples with a RNA integrity number (RIN) of 8 or greater were employed.
Each sample represents equal amount of total RNA from three mice that were pooled prior to library construction. RNAseq libraries were constructed in the center for Genomic Technologies using Trueseq RNA Library preparation kit according to Illumina protocol and sequenced with the Illumina Nextseq 500 System to an average depth of around 30 million reads.

treatment_protocol: Mice were sacrificed and liver tissues were snap frozen in liquid nitrogen.

value: Wild type


title: 6-month-3


title: AD, MTG sample 05--11

description:
Alzheimer's MTG sample
MTG 05--11

source_name: MTG sample 05--11


title: AD, MTG sample 06--42

description:
Alzheimer's MTG sample
MTG 06--42

source_name: MTG sample 06--42


title: AD, MTG sample 06--52

description:
Alzheimer's MTG sample
MTG 06--52

source_name: MTG sample 06--52


title: AD, MTG sample 98--30

description:
Alzheimer's MTG sample
MTG 98--30

source_name: MTG sample 98--30


title: 3-weeks-2

value: 3-4 weeks


title: 3-weeks-3


title: AD, MTG sample 96--11

description:
Alzheimer's MTG sample
MTG 96--11

source_name: MTG sample 96--11

value: M


title: RNA.DMSO.Untreated.R3

description: Counts Table - Acetate.txt


title: AD, MTG sample 99--15

description:
Alzheimer's MTG sample
MTG 99--15

source_name: MTG sample 99--15


title: AD, MTG sample 99--61

description:
Alzheimer's MTG sample
MTG 99--61

source_name: MTG sample 99--61


title: AD, MTG sample 99--24

description:
Alzheimer's MTG sample
MTG 99--24

source_name: MTG sample 99--24


title: AD, MTG sample 99--34

description:
Alzheimer's MTG sample
MTG 99--34

source_name: MTG sample 99--34


title: AD, MTG sample 00--47

description:
Alzheimer's MTG sample
MTG 00--47

source_name: MTG sample 00--47


title: RNase P and tmRNA in-cell plusDMS

city: Houston

first: Anthony

middle: M

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

description: Sequencing was done in a single batch with 2x150 PE sequencing. RNase P and tmRNA amplicons share the same sequencing index. fastq files also contain additional reads from unrelated experiments that do not overlap rnpB or tmRNA. Sequences were aligned against rnpB.fa and tmRNA.fa

data_processing:
ShapeMapper (v2.1.4) was used to align and parse mutations from DMS-MaP sequencing data. The --amplicon option was used for amplicon datasets, which masks out primer regions and filters out spurious reads that do not align at the expected 5' and 3' primer sites. The --random-primer-len 9 option was used to mask RT primer sites in randomly primed datasets (16S and 23S rRNAs). The --output-parsed option was used to generate parsed mutation files.
PairMapper (v1.0) was used compute normalized DMS reactivity profiles and identify correlated nucleotides from ShapeMapper-generated parsed mutation files using default parameters.
Genome_build: Sequences used for alignments are noted in SAMPLE description field and are provided as supplementary files

organism: Escherichia coli

source_name: liquid cell culture

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.
Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using ethanol precipitation prior to reverse transcription.
Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 10 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 9 uL 2.22x MaP buffer [1x MaP buffer consists of 6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0), 75 mM KCl, 10 mM DTT] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL SuperScript II Reverse Transcriptase (Invitrogen) was added and the RT reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10x[50 °C for 2 min,  42 °C for 2 min], 72 °C for 10 min. For the adenine riboswitch, ~1 pmol RNA was input into RT. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.

treatment_protocol: Exponential E. coli cultures were treated for 20 minutes with rifampicin, pelleted, resuspended in 300 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2, and modified with 680 mM DMS for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.

tag: probing condition

value: in-cell


title: rRNA in-cell minusDMS

description: Sequencing was done in 2 batches with 2x300 PE sequencing. Data from the 2 runs were merged using ShapeMapper (by placing in the same folder). Seqeunces were aligned against ec16S.fa and ec23S.fa

extract_protocol:
Reverse-transcription was performed using random 9mers, and DNA libraries were generated using a Nextera protocol.
Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using ethanol precipitation prior to reverse transcription.
Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 10 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 9 uL 2.22x MaP buffer [1x MaP buffer consists of 6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0), 75 mM KCl, 10 mM DTT] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL SuperScript II Reverse Transcriptase (Invitrogen) was added and the RT reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10x[50 °C for 2 min,  42 °C for 2 min], 72 °C for 10 min. For the adenine riboswitch, ~1 pmol RNA was input into RT. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.

treatment_protocol: Exponential E. coli cultures were treated for 20 minutes with rifampicin, pelleted, resuspended in 300 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2, and treated with 10% ethanol (final vol/vol) for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.


title: 5S, rpsB, rpsM in-cell plusDMS

description: Sequencing was done in a single batch with 2x150 PE sequencing. 5S rRNA, rpsB, rpsM amplicons share the same sequencing index. Sequences were aligned against 5S.fa, rpsB.fa, and rpsM.fa


title: RNase P and tmRNA in-cell minusDMS


title: rRNA in-cell plusDMS


title: AD, MTG sample 04--06

description:
Alzheimer's MTG sample
MTG 04--06

source_name: MTG sample 04--06


title: 6-month-1


title: AD, MTG sample 01--22

description:
Alzheimer's MTG sample
MTG 01--22

source_name: MTG sample 01--22


title: AD, MTG sample 03--37

description:
Alzheimer's MTG sample
MTG 03--37

source_name: MTG sample 03--37


title: rpsB and rpsM cell-free plusDMS

description: Sequencing was done in a single batch with 2x150 PE sequencing. rpsM and rpsB leader amplicons share the same sequencing index. fastq files also contain additional reads from unrelated experiments that do not overlap rpsB or rpsM. Sequences were aligned against rpsB.fa and rpsM.fa

treatment_protocol: Cell-free RNA from E. coli was obtained by gently extracting total RNA from exponential E. coli cultures that had been treated for 20 minutes with rifampicin to chase RNAs and RNA-protein complexes to fully assembled states. Cell-free RNA was equilibrated in 200 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2 and modified with 170 mM DMS for 6 minutes at 37 °C.

value: cell-free


title: AD, MTG sample 02--09

description:
Alzheimer's MTG sample
MTG 02--09

source_name: MTG sample 02--09


title: rpsB and rpsM cell-free minusDMS

treatment_protocol: Cell-free RNA from E. coli was obtained by gently extracting total RNA from exponential E. coli cultures that had been treated for 20 minutes with rifampicin to chase RNAs and RNA-protein complexes to fully assembled states. Cell-free RNA was equilibrated in 200 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2 and treated with 10% ethanol (final vol/vol) for 6 minutes at 37 °C.


title: tmRNA cell-free plusDMS

description: Sequencing was done in 2 batches with 2x300 PE sequencing. Data from the 2 runs were merged using ShapeMapper (by placing in the same folder). Note that fastq files contain additional reads from unrelated experiment that shared the same sequencing index but do not map to tmRNA. Sequences were aligned to tmRNA.fa


title: tmRNA cell-free minusDMS


title: AD, MTG sample 03--34

description:
Alzheimer's MTG sample
MTG 03--34

source_name: MTG sample 03--34


title: 3-weeks-1

source_name: Liver


title: AD, MTG sample 08--37

description:
Alzheimer's MTG sample
MTG 08--37

source_name: MTG sample 08--37


title: AD, MTG sample 02--35

description:
Alzheimer's MTG sample
MTG 02--35

source_name: MTG sample 02--35


title: RNase P cell-free plusDMS

description: Sequencing was done in 2 batches with 2x300 PE sequencing. Data from the 2 runs were merged using ShapeMapper (by placing in the same folder). Note that fastq files contain additional reads from unrelated experiment that shared the same sequencing index but do not map to rnpB RNA. Sequences were aligned to rnpB.fa


title: RNase P cell-free minusDMS


title: AD, MTG sample 99--53

description:
Alzheimer's MTG sample
MTG 99--53

source_name: MTG sample 99--53


title: AD, MTG sample 07--16

description:
Alzheimer's MTG sample
MTG 07--16

source_name: MTG sample 07--16


title: 5S rRNA cell-free minusDMS

description: Sequencing was done in 2 batches with 2x150 PE sequencing. Data from the 2 runs were merged using ShapeMapper (by placing in the same folder). Note that fastq files contain additional reads from unrelated experiment that shared the same sequencing index but do not map to 5S rRNA. Sequences were aligned to 5S.fa


title: 5S, rpsB, rpsM in-cell minusDMS


title: 5S rRNA cell-free plusDMS


title: AD, MTG sample 07--49

description:
Alzheimer's MTG sample
MTG 07--49

source_name: MTG sample 07--49


title: AD, MTG sample 07--34

description:
Alzheimer's MTG sample
MTG 07--34

source_name: MTG sample 07--34


title: Total RNA cell-free plusDMS

description: Sequencing was done in 3 batches with 2x300 PE sequencing. Data from the 3 runs were merged using ShapeMapper (by placing in the same folder) and aligned against ec16S.fa and ec23S.fa


title: AD, MTG sample 01--48

description:
Alzheimer's MTG sample
MTG 01--48

source_name: MTG sample 01--48


title: Total RNA cell-free minusDMS


title: AD, MTG sample 03--18

description:
Alzheimer's MTG sample
MTG 03--18

source_name: MTG sample 03--18


title: AD, MTG sample 03--01

description:
Alzheimer's MTG sample
MTG 03--01

source_name: MTG sample 03--01


title: AD, MTG sample 96--18

description:
Alzheimer's MTG sample
MTG 96--18

source_name: MTG sample 96--18


title: AD, MTG sample 92--17

description:
Alzheimer's MTG sample
MTG 92--17

source_name: MTG sample 92--17


title: AD, MTG sample 95--18

description:
Alzheimer's MTG sample
MTG 95--18

source_name: MTG sample 95--18


title: AD, MTG sample 96--29

description:
Alzheimer's MTG sample
MTG 96--29

source_name: MTG sample 96--29


title: AD, MTG sample 95--31

description:
Alzheimer's MTG sample
MTG 95--31

source_name: MTG sample 95--31


title: AD, MTG sample 96--43

description:
Alzheimer's MTG sample
MTG 96--43

source_name: MTG sample 96--43


title: AD, MTG sample 96--05

description:
Alzheimer's MTG sample
MTG 96--05

source_name: MTG sample 96--05


title: AD, MTG sample 03--52

description:
Alzheimer's MTG sample
MTG 03--52

source_name: MTG sample 03--52


title: AD, MTG sample 97--22

description:
Alzheimer's MTG sample
MTG 97--22

source_name: MTG sample 97--22


title: AD, MTG sample 04--09

description:
Alzheimer's MTG sample
MTG 04--09

source_name: MTG sample 04--09


title: AD, MTG sample 97--21

description:
Alzheimer's MTG sample
MTG 97--21

source_name: MTG sample 97--21


title: AD, MTG sample 04--49

description:
Alzheimer's MTG sample
MTG 04--49

source_name: MTG sample 04--49


title: B16F0 cells cultured for 24 hr in serum-free media, rep 1

type: RNA

city: Morgantown

first: David

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

hyb_protocol: The 21.5 microl of biotin-labeled RNA with added hybridization controls was hybridized to the GeneChip miRNA 2.0 Arrays (Affymetrix) at 48oC and 60 rpm for 16 hours in GeneChip Hybridization Oven 640 (Affymetrix).The entire reaction of fragmented and biotin-labeled cDNA (50 mu) with added hybridization controls was hybridized to the mouse GeneChip 1.0 ST Exon Arrays (Affymetrix) at 45oC for 17 hours in GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: GeneChip miRNA 2.0 Arrays were stained using FS 450_0003 protocol in Affymetrix GeneChip Fluidics Station 450. Briefly, biotin-labeled RNA was reacted using washes with a solution containing a streptavidin-phycoerythrin complex, with an intermediate treatment of biotin-labeled anti-streptadvidin antibody to amplify the signal. Phycoerythrin labeling was detected within the Affymetrix GeneChip Scanner 3000 7G plus using 532 nm light and detected by a photomultiplier tube.

data_processing: A miRNA QC Tool software (Affymetrix) was used to check quality controls of hybridized chips.  All chips that passed quality controls were RMA normalized using miRNA QC Tool.

label: biotin

source_name: B16F0 cells

label_protocol: Four hundred nanograms of each miRNA sample was biotin labeled using the Genisphere FlashTag HSR Kit according to the manufacturer's instructions. The labeling of RNA was confirmed by Enzyme Linked Oligosorbent Assay (ELOSA) according Genisphere FlashTag HSR protocol.

growth_protocol: Cultured for 24 hours in serum-free media

extract_protocol: Total RNA isolated from B16F0 exosomes and cells by RNeasy kit (Qiagen) was quantified using Nanodrop and analyzed by on-chip-electrophoresis using the Agilent Bioanalyzer.

treatment_protocol: not applicable

tag: tag


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 1

description: exosomal RNA

source_name: B16F0 exosomes


title: B16F0 cells cultured for 24 hr in serum-free media, rep 3


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 2

description: exosomal RNA


title: B16F0 cells cultured for 24 hr in serum-free media, rep 2


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 3

description: exosomal RNA


title: B16F0 cells cultured for 24 hr in serum-free media, rep 4


title: AD, MTG sample 99--48

description:
Alzheimer's MTG sample
MTG 99--48

source_name: MTG sample 99--48


title: AD, MTG sample 99--21

description:
Alzheimer's MTG sample
MTG 99--21

source_name: MTG sample 99--21


title: AD, MTG sample 98--18

description:
Alzheimer's MTG sample
MTG 98--18

source_name: MTG sample 98--18


title: B16F0 exosomes isolated from serum-free media media conditioned by B16F0 cells for 24 hr, rep 4

description: exosomal RNA


title: Brain_SC_Male_rep4

city: Guangzhou

first: Wenjun

last: Shi

address: South China Normal University, Guangzhou 510006, China

country: China

institute: The Environmental Research Institute, MOE Key Laboratory of Environmental Theoretical Chemistry

description: Gene expression after dydrogesterone  140 dpf exposure in brain

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Danio rerio

source_name: Brain, solvent control, 140 dpf, rep4

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: dydrogesterone treatment

value: solvent control

value: Brain

value: Male

value: 140 dpf


title: AD, MTG sample 00--22

description:
Alzheimer's MTG sample
MTG 00--22

source_name: MTG sample 00--22

tag: plate


title: Brain_H_Male_rep4

source_name: Brain, high concentration, 140 dpf,rep4

value: high concentration


title: Brain_L_Male_rep4

source_name: Brain, low concentration, 140 dpf,rep4

value: low concentration


title: Brain_M_Male_rep3

source_name: Brain, medium concentration, 140 dpf,rep3

value: medium concentration


title: Brain_H_Male_rep3

source_name: Brain, high concentration, 140 dpf,rep3


title: Brain_L_Male_rep3

source_name: Brain, low concentration, 140 dpf,rep3


title: AD, MTG sample 03--06

description:
Alzheimer's MTG sample
MTG 03--06

source_name: MTG sample 03--06

tag: bead chip

value: brain

value: MTG

value: F


title: Brain_L_Male_rep2

source_name: Brain, low concentration, 140 dpf,rep2


title: Brain_H_Male_rep2

source_name: Brain, high concentration, 140 dpf,rep2


title: AD, MTG sample 06--37

description:
Alzheimer's MTG sample
MTG 06--37

source_name: MTG sample 06--37

tag: well position

value: AD


title: AD, MTG sample 99--41

description:
Alzheimer's MTG sample
MTG 99--41

source_name: MTG sample 99--41

tag: tissue


title: AD, MTG sample 02--39

description:
Alzheimer's MTG sample
MTG 02--39

source_name: MTG sample 02--39

tag: brain region


title: AD, MTG sample 07--12

description:
Alzheimer's MTG sample
MTG 07--12

source_name: MTG sample 07--12

tag: gender


title: Brain_M_Male_rep2

source_name: Brain, medium concentration, 140 dpf,rep2

tag: age


title: AD, MTG sample 07--21

description:
Alzheimer's MTG sample
MTG 07--21

source_name: MTG sample 07--21

tag: diagnosis


title: AD, MTG sample 07--71

description:
Alzheimer's MTG sample
MTG 07--71

source_name: MTG sample 07--71


title: AD, MTG sample 03--27

description:
Alzheimer's MTG sample
MTG 03--27

source_name: MTG sample 03--27


title: AD, MTG sample 04--32

description:
Alzheimer's MTG sample
MTG 04--32

source_name: MTG sample 04--32


title: AD, MTG sample 95--01

description:
Alzheimer's MTG sample
MTG 95--01

source_name: MTG sample 95--01


title: AD, MTG sample 97--24

description:
Alzheimer's MTG sample
MTG 97--24

source_name: MTG sample 97--24


title: AD, MTG sample 04--54

description:
Alzheimer's MTG sample
MTG 04--54

source_name: MTG sample 04--54


title: Brain_M_Male_rep1

source_name: Brain, medium concentration, 140 dpf,rep1


title: testes_H_Male_rep3

description: Gene expression after dydrogesterone  140 dpf exposure in testes

source_name: Testes, high concentration, 140 dpf,rep3

value: testes


title: AD, MTG sample 96--20

description:
Alzheimer's MTG sample
MTG 96--20

source_name: MTG sample 96--20


title: testes_H_Male_rep2

source_name: Testes, high concentration, 140 dpf,rep2


title: AD, MTG sample 98--06

description:
Alzheimer's MTG sample
MTG 98--06

source_name: MTG sample 98--06


title: Brain_L_Male_rep1

source_name: Brain, low concentration, 140 dpf,rep1


title: Brain_M_Male_rep4

source_name: Brain, medium concentration, 140 dpf,rep4


title: testes_H_Male_rep4

source_name: Testes, high concentration, 140 dpf,rep4


title: AD, MTG sample 04--16

description:
Alzheimer's MTG sample
MTG 04--16

source_name: MTG sample 04--16


title: Brain_H_Male_rep1

source_name: Brain, high concentration, 140 dpf,rep1


title: testes_M_Male_rep4

source_name: Testes, medium concentration, 140 dpf,rep4


title: Brain_SC_Male_rep2

source_name: Brain, solvent control, 140 dpf, rep2


title: testes_L_Male_rep4

source_name: Testes, low concentration, 140 dpf,rep4


title: Brain_SC_Male_rep3

source_name: Brain, solvent control, 140 dpf, rep3


title: testes_L_Male_rep3

source_name: Testes, low concentration, 140 dpf,rep3


title: Brain_SC_Male_rep1

source_name: Brain, solvent control, 140 dpf, rep1


title: testes_H_Male_rep1

source_name: Testes, high concentration, 140 dpf,rep1


title: testes_M_Male_rep3

source_name: Testes, medium concentration, 140 dpf,rep3


title: AD, MTG sample 06--65

description:
Alzheimer's MTG sample
MTG 06--65

source_name: MTG sample 06--65


title: testes_M_Male_rep2

source_name: Testes, medium concentration, 140 dpf,rep2


title: AD, MTG sample 01--12

description:
Alzheimer's MTG sample
MTG 01--12

source_name: MTG sample 01--12


title: testes_M_Male_rep1

source_name: Testes, medium concentration, 140 dpf,rep1


title: AD, MTG sample 97--39

description:
Alzheimer's MTG sample
MTG 97--39

source_name: MTG sample 97--39


title: AD, MTG sample 01--02

description:
Alzheimer's MTG sample
MTG 01--02

source_name: MTG sample 01--02


title: AD, MTG sample 98--44

description:
Alzheimer's MTG sample
MTG 98--44

source_name: MTG sample 98--44


title: AD, MTG sample 01--07

description:
Alzheimer's MTG sample
MTG 01--07

source_name: MTG sample 01--07


title: 965oxbs

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: Oxidative Bisulfite-converted

data_processing:
Adaptor timming and filtering (Basespace FASTQ Toolkit, Illumina)
Alignment (Basespace MethylSeq App, Illumina)
Coverage files used to get whole genome, X, and Y methylation and hydroxymethylation percentages in CG and non-CG contexts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark coverage text files,  with chr/start/stop/methylation percentage/ count methylated/ count unmethylated

source_name: Hippocampus

extract_protocol:
AllPrep DNA/RNA Mini kits (Qiagen, Germantown, MD)
Ovation Ultralow Methyl-Seq Library System (NuGEN, Tecan Genomics, Inc., Redwood City, CA)

tag: Sex

value: Vehicle (Sunflower Oil)

value: 3 Months


title: AD, MTG sample 01--33

description:
Alzheimer's MTG sample
MTG 01--33

source_name: MTG sample 01--33

value: M


title: AD, MTG sample 02--19

description:
Alzheimer's MTG sample
MTG 02--19

source_name: MTG sample 02--19


title: AD, MTG sample 01--21

description:
Alzheimer's MTG sample
MTG 01--21

source_name: MTG sample 01--21


title: AD, MTG sample 99--13

description:
Alzheimer's MTG sample
MTG 99--13

source_name: MTG sample 99--13


title: AD, MTG sample 00--08

description:
Alzheimer's MTG sample
MTG 00--08

source_name: MTG sample 00--08


title: 962oxbs

description: Oxidative Bisulfite-converted

value: Tamoxifen


title: AD, MTG sample 98--28

description:
Alzheimer's MTG sample
MTG 98--28

source_name: MTG sample 98--28


title: testes_L_Male_rep2

source_name: Testes, low concentration, 140 dpf,rep2


title: 963oxbs

description: Oxidative Bisulfite-converted


title: 959oxbs

description: Oxidative Bisulfite-converted


title: testes_SC_Male_rep3

source_name: Testes, solvent control, 140 dpf, rep3


title: 961oxbs

description: Oxidative Bisulfite-converted


title: testes_SC_Male_rep1

source_name: Testes, solvent control, 140 dpf, rep1


title: AD, MTG sample 08--29

description:
Alzheimer's MTG sample
MTG 08--29

source_name: MTG sample 08--29


title: AD, MTG sample 08--30

description:
Alzheimer's MTG sample
MTG 08--30

source_name: MTG sample 08--30


title: testes_SC_Male_rep2

source_name: Testes, solvent control, 140 dpf, rep2


title: 955oxbs

description: Oxidative Bisulfite-converted

value: Female


title: testes_L_Male_rep1

source_name: Testes, low concentration, 140 dpf,rep1


title: AD, MTG sample 08--48

description:
Alzheimer's MTG sample
MTG 08--48

source_name: MTG sample 08--48


title: 958oxbs

description: Oxidative Bisulfite-converted


title: AD, MTG sample 08--10

description:
Alzheimer's MTG sample
MTG 08--10

source_name: MTG sample 08--10


title: 957oxbs

description: Oxidative Bisulfite-converted


title: testes_SC_Male_rep4

source_name: Testes, solvent control, 140 dpf, rep4

value: solvent control


title: 964oxbs

description: Oxidative Bisulfite-converted

source_name: Hippocampus


title: 953oxbs

description: Oxidative Bisulfite-converted


title: AD, MTG sample 08--05

description:
Alzheimer's MTG sample
MTG 08--05

source_name: MTG sample 08--05


title: AD, MTG sample 08--22

description:
Alzheimer's MTG sample
MTG 08--22

source_name: MTG sample 08--22


title: AD, MTG sample 08--46

description:
Alzheimer's MTG sample
MTG 08--46

source_name: MTG sample 08--46


title: 951oxbs

description: Oxidative Bisulfite-converted


title: AD, MTG sample 08--89

description:
Alzheimer's MTG sample
MTG 08--89

source_name: MTG sample 08--89


title: AD, MTG sample 03--04

description:
Alzheimer's MTG sample
MTG 03--04

source_name: MTG sample 03--04


title: ND, CBL sample 03--41

description:
control CBL sample
CBL 03--41

source_name: CBL sample 03--41

value: CBL

value: ND


title: ND, CBL sample 01--51

description:
control CBL sample
CBL 01--51

source_name: CBL sample 01--51


title: 963BS

description: Bisulfite-converted

value: Male


title: ND, CBL sample 03--47

description:
control CBL sample
CBL 03--47

source_name: CBL sample 03--47


title: 964BS

description: Bisulfite-converted


title: 961BS

description: Bisulfite-converted


title: ND, CBL sample 08--40

description:
control CBL sample
CBL 08--40

source_name: CBL sample 08--40


title: 959BS

description: Bisulfite-converted


title: 954oxbs

description: Oxidative Bisulfite-converted


title: ND, CBL sample 08--04

description:
control CBL sample
CBL 08--04

source_name: CBL sample 08--04


title: 957BS

description: Bisulfite-converted


title: ND, CBL sample 06--13

description:
control CBL sample
CBL 06--13

source_name: CBL sample 06--13


title: ND, CBL sample 05--21

description:
control CBL sample
CBL 05--21

source_name: CBL sample 05--21


title: 955BS

description: Bisulfite-converted


title: 958BS

description: Bisulfite-converted


title: 954BS

description: Bisulfite-converted


title: ND, CBL sample 07--04

description:
control CBL sample
CBL 07--04

source_name: CBL sample 07--04


title: 953BS

description: Bisulfite-converted


title: ND, CBL sample 05--16

description:
control CBL sample
CBL 05--16

source_name: CBL sample 05--16


title: ND, CBL sample 07--10

description:
control CBL sample
CBL 07--10

source_name: CBL sample 07--10


title: 951BS

description: Bisulfite-converted


title: 965BS

description: Bisulfite-converted


title: R65-O

description: Oxidative Bisulfite-converted

source_name: Retina


title: ND, CBL sample 96--16

description:
control CBL sample
CBL 96--16

source_name: CBL sample 96--16


title: R64-O

description: Oxidative Bisulfite-converted


title: 962BS

description: Bisulfite-converted

source_name: Hippocampus


title: ND, CBL sample 92--32

description:
control CBL sample
CBL 92--32

source_name: CBL sample 92--32


title: R63-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 96--38

description:
control CBL sample
CBL 96--38

source_name: CBL sample 96--38


title: R62-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 92--10

description:
control CBL sample
CBL 92--10

source_name: CBL sample 92--10


title: R61-O

description: Oxidative Bisulfite-converted


title: R59-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 97--46

description:
control CBL sample
CBL 97--46

source_name: CBL sample 97--46


title: ND, CBL sample 98--22

description:
control CBL sample
CBL 98--22

source_name: CBL sample 98--22


title: R58-O

description: Oxidative Bisulfite-converted


title: R55-O

description: Oxidative Bisulfite-converted


title: R57-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 08--88

description:
control CBL sample
CBL 08--88

source_name: CBL sample 08--88


title: R53-O

description: Oxidative Bisulfite-converted


title: R54-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 96--08

description:
control CBL sample
CBL 96--08

source_name: CBL sample 96--08


title: ND, CBL sample 99--66

description:
control CBL sample
CBL 99--66

source_name: CBL sample 99--66


title: ND, CBL sample 00--15

description:
control CBL sample
CBL 00--15

source_name: CBL sample 00--15


title: R65-B

description: Bisulfite-converted


title: ND, CBL sample 06--53

description:
control CBL sample
CBL 06--53

source_name: CBL sample 06--53


title: R63-B

description: Bisulfite-converted


title: R64-B

description: Bisulfite-converted


title: ND, CBL sample 06--27

description:
control CBL sample
CBL 06--27

source_name: CBL sample 06--27


title: R62-B

description: Bisulfite-converted


title: ND, CBL sample 06--68

description:
control CBL sample
CBL 06--68

source_name: CBL sample 06--68


title: ND, CBL sample 98--27

description:
control CBL sample
CBL 98--27

source_name: CBL sample 98--27


title: ND, CBL sample 07--37

description:
control CBL sample
CBL 07--37

source_name: CBL sample 07--37


title: R58-B

description: Bisulfite-converted

source_name: Retina


title: ND, CBL sample 06--33

description:
control CBL sample
CBL 06--33

source_name: CBL sample 06--33


title: R59-B

description: Bisulfite-converted


title: ND, CBL sample 93--20

description:
control CBL sample
CBL 93--20

source_name: CBL sample 93--20


title: ND, CBL sample 92--06

description:
control CBL sample
CBL 92--06

source_name: CBL sample 92--06


title: R61-B

description: Bisulfite-converted


title: R57-B

description: Bisulfite-converted


title: R55-B

description: Bisulfite-converted


title: ND, CBL sample 02--12

description:
control CBL sample
CBL 02--12

source_name: CBL sample 02--12


title: ND, CBL sample 96--13

description:
control CBL sample
CBL 96--13

source_name: CBL sample 96--13


title: R54-B

description: Bisulfite-converted


title: ND, CBL sample 99--44

description:
control CBL sample
CBL 99--44

source_name: CBL sample 99--44


title: R51-O

description: Oxidative Bisulfite-converted


title: R53-B

description: Bisulfite-converted


title: R51-B

description: Bisulfite-converted


title: C65-O

description: Oxidative Bisulfite-converted

source_name: Cortex


title: ND, CBL sample 97--17

description:
control CBL sample
CBL 97--17

source_name: CBL sample 97--17


title: ND, CBL sample 08--83

description:
control CBL sample
CBL 08--83

source_name: CBL sample 08--83


title: C64-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 99--59

description:
control CBL sample
CBL 99--59

source_name: CBL sample 99--59


title: ND, CBL sample 03--11

description:
control CBL sample
CBL 03--11

source_name: CBL sample 03--11


title: C63-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 04--19

description:
control CBL sample
CBL 04--19

source_name: CBL sample 04--19


title: ND, CBL sample 99--50

description:
control CBL sample
CBL 99--50

source_name: CBL sample 99--50


title: C61-O

description: Oxidative Bisulfite-converted


title: C62-O

description: Oxidative Bisulfite-converted


title: C59-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 02--38

description:
control CBL sample
CBL 02--38

source_name: CBL sample 02--38


title: ND, CBL sample 05--20

description:
control CBL sample
CBL 05--20

source_name: CBL sample 05--20


title: ND, CBL sample 08--55

description:
control CBL sample
CBL 08--55

source_name: CBL sample 08--55


title: C57-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 04--31

description:
control CBL sample
CBL 04--31

source_name: CBL sample 04--31


title: C55-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 96--35

description:
control CBL sample
CBL 96--35

source_name: CBL sample 96--35


title: ND, CBL sample 05--61

description:
control CBL sample
CBL 05--61

source_name: CBL sample 05--61


title: ND, CBL sample 96--32

description:
control CBL sample
CBL 96--32

source_name: CBL sample 96--32


title: ND, CBL sample 92--05

description:
control CBL sample
CBL 92--05

source_name: CBL sample 92--05


title: ND, CBL sample 96--44

description:
control CBL sample
CBL 96--44

source_name: CBL sample 96--44


title: ND, CBL sample 98--19

description:
control CBL sample
CBL 98--19

source_name: CBL sample 98--19


title: C54-O

description: Oxidative Bisulfite-converted

source_name: Cortex


title: ND, CBL sample 97--14

description:
control CBL sample
CBL 97--14

source_name: CBL sample 97--14


title: ND, CBL sample 07--26

description:
control CBL sample
CBL 07--26

source_name: CBL sample 07--26


title: C63-B

description: Bisulfite-converted


title: C51-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 03--66

description:
control CBL sample
CBL 03--66

source_name: CBL sample 03--66


title: C65-B

description: Bisulfite-converted


title: C64-B

description: Bisulfite-converted


title: C53-O

description: Oxidative Bisulfite-converted


title: ND, CBL sample 02--36

description:
control CBL sample
CBL 02--36

source_name: CBL sample 02--36


title: C61-B

description: Bisulfite-converted


title: C59-B

description: Bisulfite-converted


title: ND, CBL sample 03--10

description:
control CBL sample
CBL 03--10

source_name: CBL sample 03--10


title: C58-B

description: Bisulfite-converted


title: C58-O

description: Oxidative Bisulfite-converted


title: C57-B

description: Bisulfite-converted


title: ND, CBL sample 04--08

description:
control CBL sample
CBL 04--08

source_name: CBL sample 04--08


title: ND, CBL sample 01--44

description:
control CBL sample
CBL 01--44

source_name: CBL sample 01--44


title: C55-B

description: Bisulfite-converted


title: ND, CBL sample 07--70

description:
control CBL sample
CBL 07--70

source_name: CBL sample 07--70


title: ND, CBL sample 07--46

description:
control CBL sample
CBL 07--46

source_name: CBL sample 07--46


title: C54-B

description: Bisulfite-converted


title: C53-B

description: Bisulfite-converted


title: C51-B

description: Bisulfite-converted


title: ND, CBL sample 07--52

description:
control CBL sample
CBL 07--52

source_name: CBL sample 07--52


title: C62-B

description: Bisulfite-converted


title: ND, CBL sample 04--30

description:
control CBL sample
CBL 04--30

source_name: CBL sample 04--30


title: esc_cd4T_Cscreen

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
CRISPRscreen
siRNA
processed data file: esc_Cscreen_res.txt

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ATAC-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragment and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer running with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer between the end of the primer and the restriction sites used in the corresponding experiment.
4C-Seq: mapping: bowtie-1.1.1/bowtie -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to NlaIII/CSP6i fragment (human) or DpnII/CSP6i fragment (mouse)to calculate fraction of restriction fragments for which 4C reads were found
CRISPR screen: Build artificial genome with primer and sgRNA constructs and make index with bowtie
CRISPR screen: alignment: bowtie -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: filtering and sort: samtools view -S -b -F4 | samtools sort -@ 2
CRISPR screen: samtools idxstats on aligned file
CRISPR screen: calculate frequency of each sgRNAs in each pool
CRISPR screen: samtools idxstats on aligned file
Genome_build: mm9 (MGSCv37), hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh.
Supplementary_files_format_and_content: 4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window.
Supplementary_files_format_and_content: mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: CRISPRscreen: summarized text file on each codition, replicates, gene, sgRNAs.

source_name: CD4+ T cell, ES cell (spleen, blastocyst)

growth_protocol: Cas9 expressing cells: Primary CD4+ cells expressing Cas9 were isolated from a Cas9 expressing mouse (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh) (Platt et al., Cell, 2014). Spleen was triturated in DMEM, supernatant was filtered and immediately processed according to the MACS mouse CD4+ T Cell Isolation Kit (Miltenyi Biotec, Cologne, Germany), following the manufacturer’s protocol. Isolated cells were seeded in a six-well plate that was previously coated with aCD3 and aCD28 at a final concentration of 10 ug/mL in 1.6 mL of PBS. The plate was incubated at 37°C for a minimum of 30 min. The PBS was then removed and the cells added to the plate. Cas9 expression in E14 ES cells was obtained through infection with lentiCas9-blast virus (Addgene plasmid #52962). After Blasticidin selection (7.5 ug/mL), clones expressing Cas9 were isolated and expanded to be used for the multiCRISPR screen for essential Mediator subunits. Cas9 expression was assessed by Western blot analysis and cutting efficiency after transfection with sgRNA plasmids.

extract_protocol:
Extraction protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with MNase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or MNase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x10^7 resting and activated B cells were digested with 24 different concentrations of MNaseI. After an initial RT-qPCR analysis and curve-fitting, the MNaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MNaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MNaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: We used the same protocol for in situ HiC libraries as Rao et al., (Cell, 2014 Dec; 159:1-16).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7 ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C. Bait was amplified with inverse PCR primers as follows: 3RR with DpnII: _4C 5′- GCTTATCTGTAAAGAATGGGTC-3′, 3RR_Csp6i 5′-GGCCTTAGAAGGCTCTGTAC-3′. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 10^6 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated. ERCC-spike-in was added on some samples for quantitative comparison between two conditions.
ATACseq: One hundred thousand cultured cells were harvested for each point. Cell lysis and Transposition reaction were immediately performed according to Greenleaf’s group protocol (Corces et al., Nat Meth 2017; Buenrostro et al., Nat Meth 2013). Transposed DNA was immediately purified and stored at -20C before library preparation according to the above protocol.
CRISPRscreen: Cells were harvested at an early reference time-point (second day after infection) and two late time-points (14 and 21 days after infection). DNA was extracted using DNeasy Blood and tissue kit according to the manufacturer’s instructions (#69506, Qiagen).
Library construction protocol:
ChIP-Seq  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2500 or 3000 (Illumina).
HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
4C-seq: DNA was prepared for paired-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 2000, 2500 or 3000 (Illumina).
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).
CRISPRscreen: DNA was prepared for single-end Illumina sequencing using staggered GeCKO readout primers (Shalem et al. 2013). 80 cycles of sequencing data were acquired on the MiSeq (Illumina).

treatment_protocol: CRISPR infection: The viral libraries which contain sgRNAs were used to infect Cas9 expressing E14 ES cells and primary CD4+ T cells isolated from the Rosa26-Cas9 expressing mice. Two hundred thousand cells were seeded in a six-well plate the day before infection. Concentrated viruses were added to the media in presence of Polybrene (6 ug/mL). The amount of virus was adjusted according to the viral titer to obtain a MOI of 0.3. Cells were transduced by spinfection at 1,350g for 90 min and 28-32°C. Infected cells were selected 24h after infection, using Puromycin at a final concentration of 1 ug/ml for ES cells and 2 ug/mL for CD4+ T cells.

tag: cell line

value: Primary CD4+ T cells, ES cell line

tag: genotype/variation

value: WT


title: esc_Cscreen

source_name: ES cell (blastocyst)

value: ES cell line


title: ch12_wt_chipseq_H3K36me3_APR48h

data_processing:
base calling: illumina CASAVA 1.8.2
Promter Capture HiC-Seq: alignment: bowtie 2.3.4.3 with default parameter to hg19
Promter Capture HiC-Seq: alignment and filter: HiCUP v0.5.9
Promter Capture HiC-Seq: Normalization: randomly selecting enough reads in order to obtain 73 million read pairs in cis and >10 b apart from each bait
Promter Capture HiC-Seq: Interaction call: with default parameter by using CHiCAGO 1.10.1
BSseq:triming: remove first 8nt with cutadapt program
BSseq:alignment: aliged to mm9 with default parameter using Bismark
BSseq:filter: low quality sequences and PCR duplicates are removed by BSseeker2
BSseq:bedgraph generation: bismark_methylation_extractor in Bismark pacakge
Genome_build: mm9, hg19
Supplementary_files_format_and_content: Promter Capture HiC-Seq: .txt file generated by CHiCAGO for significant interaction calls
Supplementary_files_format_and_content: BSseq:bedgraph to show the methylation %

source_name: CH12 B cell line

extract_protocol:
Promoter Capture  HiC-Seq:  we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7)                                                                                BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer’s protocol.
Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina).                                                                                BS-seq: standard RNA-Seq   library   preparation   was performed following  the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)

tag: genotype

value: lymphoma cell line

tag: chip antibody

value: Abcam, ab9050

tag: treatment


title: ND, CBL sample 06--32

description:
control CBL sample
CBL 06--32

source_name: CBL sample 06--32

value: brain

value: F


title: ch12_Med14Nsmash_chipseq_H3K36me3_APR48h

tag: cell type


title: ND, CBL sample 06--66

description:
control CBL sample
CBL 06--66

source_name: CBL sample 06--66


title: ND, CBL sample 06--43

description:
control CBL sample
CBL 06--43

source_name: CBL sample 06--43


title: ch12_Med14Nsmash_chipseq_H3K4me1_APR48h

value: Abcam, ab8895


title: ch12_Med14Nsmash_chipseq_PolIIS2P_APR0h

value: Abcam. Ab5095


title: ND, CBL sample 93--07

description:
control CBL sample
CBL 93--07

source_name: CBL sample 93--07


title: ch12_wt_chipseq_H3K4me1_APR48h


title: ND, CBL sample 96--28

description:
control CBL sample
CBL 96--28

source_name: CBL sample 96--28


title: ND, CBL sample 94--35

description:
control CBL sample
CBL 94--35

source_name: CBL sample 94--35


title: ND, CBL sample 98--32

description:
control CBL sample
CBL 98--32

source_name: CBL sample 98--32


title: ND, CBL sample 97--03

description:
control CBL sample
CBL 97--03

source_name: CBL sample 97--03


title: ND, CBL sample 97--09

description:
control CBL sample
CBL 97--09

source_name: CBL sample 97--09


title: ND, CBL sample 08--64

description:
control CBL sample
CBL 08--64

source_name: CBL sample 08--64


title: ND, CBL sample 97--45

description:
control CBL sample
CBL 97--45

source_name: CBL sample 97--45


title: ND, CBL sample 08--77

description:
control CBL sample
CBL 08--77

source_name: CBL sample 08--77


title: ch12_wt_chipseq_H3K27ac_br2

value: Abcam. ab4729


title: Drop-seq [Batch 4]

city: Chapel Hill

first: Marcus

middle: Luis

last: Basiri

state: NC

address: 115 Mason Farm Road

institute: UNC Chapel Hill

description: Internal sample name: BI

data_processing:
Demultiplexing was performed with 1 mismatch allowed using Illumina bcl2fastq v2.18.0.12.
Read 2 was aligned to mm10 using STAR v2.4.2a with 72 GB of RAM and 16 threads.
Aligned reads were tagged with mate-pair UMI and cell barcodes using Drop-seq_tools v1.12 and Picard Tools v2.2.4.
Aligned exonic reads were tagged with a mapped gene name.
A count expression matrix was made by counting UMIs for each gene for each cell barcode.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Processed gene count expression matrices are provided for each sample.

source_name: BNST tissue punch

growth_protocol: Animals were housed on a reverse 12 hr./12 hr. day/light cycle with ad libitum access to standard chow and water.

extract_protocol:
Single cell suspensions were prepared from BNST tissue punches and processed through the standard DropSeq protocol to generate single-cell cDNA libraries attached to barcoded beads. Beads were counted, PCR amplified and indexed at the 3' end for sequencing using a modified Nextera XT protocol. The pooled library was sequenced on an Illumina HiSeq 2500 in rapid-run mode using paired-end sequencing with 20x8x50 cycles.
Drop-seq

tag: strain/background

value: Wildtype

value: Bed nucleus of stria terminalis (BNST)


title: Drop-seq [Batch 3]

description: Internal sample name: BH


title: Drop-seq [Batch 1]

description: Internal sample name: BF


title: Drop-seq [Batch 2]

description: Internal sample name: BG


title: mESC_rpf_Trim71KO_batch2_rep2

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
2K2

data_processing:
Library strategy: Ribo-seq
Basecalling was performed using RTA v. 1.13.48.
Reads from mouse samples were aligned to the mm10 genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with default settings, or using the STAR aligner with the following settings: —outFileterType BySJout, —outFilterMultimapNmax 20, —outMultimapperOrder Random, —outSAMmultNmax 1, —alignSJoverhangMin 8, —alignSJDBoverhangMin 1,  —alignIntronMin 20, —alignIntronMax 1000000
Reads from human samples were aligned to the hg19 genome assembly using the STAR aligner, with the same settings as above.
Gene expression was quantified using Ensembl annotations for mouse and UCSC known Gene annotations for human, downloaded from Bioconductor (“TxDb.Mmusculus.UCSC.mm10.ensGene” and “TxDb.Hsapiens.UCSC.hg19.knownGene”). The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Ensembl identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample. HuH7 file: first column contains Entrez IDs, second column contains gene symbols, following columns as in other files.

growth_protocol: Mouse embryonic stem cells (129xC57BL/6 Rosa26Cre-ERT2/BirA-V5 [cMB063 (Ostapcuk et al., 2018)]) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.   Ne4C cells (ATCC® CRL-2925™ (Schlett and Madarasz, 1997)) were cultured on poly-l-lysine coated dishes in Ne4C medium (DMEM [Gibco; 11885084] supplemented with 10% fetal bovine serum [Sigma], 2mM L-glutamine [Gibco; 25030081], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.   Huh-7 cells (JCRB0403 (Nakabayashi et al., 1982)) were cultured in Huh-7 medium (DMEM [Gibco; 31966021] supplemented with 10% fetal bovine serum [Sigma] 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.

extract_protocol:
TriZol
TruSeq small RNA kit [Illumina; RS-200] adjusted as described in (Aeschimann et al., 2015)

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71-/-

value: mESC

tag: strain

value: Rosa26Cre-ERT2/BirA-V5 TRIM71-/-


title: mESC_rpf_WT_batch2_rep2

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
2W2


title: ch12_wt_chipseq_H3K27ac_br1


title: CD11cCre-Wnt4flox/flox CD11c+ bone marrow cells

first: Herbert

middle: R

last: De'Broski

address: 3800 Spruce St

institute: University of Pennsylvania

data_processing:
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98  nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
Alignment, barcode assignation, and generation of cell-gene-count matrices were performed using CellRanger 2.1.0 from 10x Genomics
We obtained 36,627 reads from WT and 51,048 reads from CD11cCre-Wnt4flox/flox (KO) per cell with a median genes per cell of 715 for WT and 957 for KO and median UMI count per cell of 2,639 for WT and 2,832 for KO.
CellRanger output was analyzed using Seurat v3.0.0 (https://satijalab.org/seurat/). Briefly, the datasets were filtered to keep genes that were identified in at least 3 cells and to only retain cells with at least 200 genes. The WT and KO datasets were then merged, normalized, and variable genes were identified using a mean variance selection method.
Genome_build: mm10
Supplementary_files_format_and_content: cell-gene-matrices were generated from CellRanger 2.1.0

source_name: Primary bone marrow cells

extract_protocol:
The CD11c+ magnetically-enriched bone marrow cells were loaded onto a GemCode instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell barcoded droplets (GEMs)
Single cell libraries were prepared using the 10x Genomics Chromium Single Cell 3' Solution v2 kit according to the manufacturer's instructions. The resulting libraries were sequenced across two lanes on an Illumina HiSeq2500 instrument in High-output mode.
Chromium 10x Single Cell 3' v2

treatment_protocol: Primary bone marrow cells after red blood cell lysis were subjected to CD11c MicroBeads (Miltenyi Biotec, Germany) magnetic enrichment.

value: Primary bone marrow cells

tag: cell subpopulation

value: CD11c+ cells


title: mESC_rpf_Trim71KO_batch2_rep1

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
2K1


title: mESC_rpf_WT_batch2_rep1

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
2W1


title: ch12_Tailless_chipseq_H3K27ac_br1


title: ND, CBL sample 95--34

description:
control CBL sample
CBL 95--34

source_name: CBL sample 95--34

tag: plate

tag: bead chip

value: CBL

value: M

value: ND


title: mESC_rpf_Trim71KO_batch1_rep2

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
1K2


title: ch12_wt_mRNA_spikein_br3

description: ercc-spike-in

value: WT


title: ND, CBL sample 04--26

description:
control CBL sample
CBL 04--26

source_name: CBL sample 04--26

tag: well position

tag: tissue


title: ND, CBL sample 03--17

description:
control CBL sample
CBL 03--17

source_name: CBL sample 03--17

tag: brain region

tag: gender


title: mESC_rpf_Trim71KO_batch1_rep1

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
1361X3


title: ch12_wt_mRNA_spikein_br2

description: ercc-spike-in

source_name: CH12 B cell line

value: lymphoma cell line


title: Ne4C_Trim71KO_exp3_rep2

description:
Ne4C_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
Ne4C KO2

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads from mouse samples were aligned to the mm10 genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with default settings, or using the STAR aligner with the following settings: —outFileterType BySJout, —outFilterMultimapNmax 20, —outMultimapperOrder Random, —outSAMmultNmax 1, —alignSJoverhangMin 8, —alignSJDBoverhangMin 1,  —alignIntronMin 20, —alignIntronMax 1000000
Reads from human samples were aligned to the hg19 genome assembly using the STAR aligner, with the same settings as above.
Gene expression was quantified using Ensembl annotations for mouse and UCSC known Gene annotations for human, downloaded from Bioconductor (“TxDb.Mmusculus.UCSC.mm10.ensGene” and “TxDb.Hsapiens.UCSC.hg19.knownGene”). The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Ensembl identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample. HuH7 file: first column contains Entrez IDs, second column contains gene symbols, following columns as in other files.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)


title: Ne4C_Trim71KO_exp3_rep1

description:
Ne4C_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
Ne4C KO1


title: WT CD11c+ bone marrow cells


title: ND, CBL sample 96--03

description:
control CBL sample
CBL 96--03

source_name: CBL sample 96--03

tag: age

tag: diagnosis


title: Ne4C_WT_exp3_rep2

description:
Ne4C_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
Ne4C WT2

treatment_protocol: Ne4C CRL-2925


title: ND, CBL sample 04--11

description:
control CBL sample
CBL 04--11

source_name: CBL sample 04--11


title: Ne4C_WT_exp3_rep1

description:
Ne4C_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
Ne4C WT1


title: ch12_wt_mRNA_spikein_br1

description: ercc-spike-in


title: ch12_wt_BS_br2


title: ch12_wt_BS_br1


title: Ne4C_Trim71KO_exp2_rep1

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
K1


title: Ne4C_WT_exp2_rep3

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
W3


title: ch12_Tailless_chipseq_H3K27ac_br2


title: mESC_rpf_WT_batch1_rep2

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
1W2


title: Ne4C_WT_exp2_rep2

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
W2


title: ND, CBL sample 07--58

description:
control CBL sample
CBL 07--58

source_name: CBL sample 07--58


title: Ne4C_WT_exp2_rep1

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
W1


title: Ne4C_Trim71KO_exp1_rep2

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C K2


title: Ne4C_Trim71KO_exp1_rep3

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C K3


title: ch12_Tailless_mRNA_spikein_br3

description: ercc-spike-in


title: ND, CBL sample 08--35

description:
control CBL sample
CBL 08--35

source_name: CBL sample 08--35


title: mESC_rpf_WT_batch1_rep1

description:
trim71_riboseq_CDS_counts.tab
sample name in processed data file:
1361X1


title: Ne4C_WT_exp1_rep3

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C W3


title: ch12_Tailless_mRNA_spikein_br1

description: ercc-spike-in


title: ND, CBL sample 01--37

description:
control CBL sample
CBL 01--37

source_name: CBL sample 01--37


title: Ne4C_Trim71KO_exp2_rep3

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
K3


title: ch12_Tailless_mRNA_spikein_br2

description: ercc-spike-in


title: Ne4C_WT_exp1_rep2

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C W2


title: ND, CBL sample 00--49

description:
control CBL sample
CBL 00--49

source_name: CBL sample 00--49


title: Ne4C_Trim71KO_exp2_rep2

description:
Ne4C_totalRNA_exon_counts.tab
sample name in processed data file:
K2


title: ND, CBL sample 07--28

description:
control CBL sample
CBL 07--28

source_name: CBL sample 07--28


title: ND, CBL sample 08--47

description:
control CBL sample
CBL 08--47

source_name: CBL sample 08--47


title: ND, CBL sample 07--30

description:
control CBL sample
CBL 07--30

source_name: CBL sample 07--30


title: mESC_Trim71RING_LIF_exp2_rep2

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_R2

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71C12AC15A/C12AC15A


title: ch12_Tailless_BS_br2


title: mESC_Trim71RING_LIF_exp2_rep1

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_R1


title: Ne4C_WT_exp1_rep1

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C W1


title: ch12_Tailless_BS_br1


title: ND, CBL sample 06--63

description:
control CBL sample
CBL 06--63

source_name: CBL sample 06--63


title: mESC_Trim71NHL_LIF_exp2_rep1

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_N1

treatment_protocol: mES (129xC57BL/6) Rosa26Cre-ERT2/BirA-V5 TRIM71R738A/R738A


title: mESC_Trim71NHL_LIF_exp2_rep2

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_N2


title: ch12_Med23mm_mRNA_spikein_br3

description: ercc-spike-in


title: ND, CBL sample 06--19

description:
control CBL sample
CBL 06--19

source_name: CBL sample 06--19


title: mESC_Trim71KO_LIF_exp2_rep2

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_K2


title: Ne4C_Trim71KO_exp1_rep1

description:
trim71_Ne4C_mRNA_counts.tab
sample name in processed data file:
Ne4C K1


title: mESC_Trim71KO_LIF_exp2_rep1

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_K1


title: ch12_Med23mm_mRNA_spikein_br1

description: ercc-spike-in


title: ND, CBL sample 06--25

description:
control CBL sample
CBL 06--25

source_name: CBL sample 06--25


title: mESC_WT_LIF_exp2_rep2

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_W2


title: mESC_WT_LIF_exp2_rep1

description:
trim71_1705F_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF_W1


title: ND, CBL sample 05--36

description:
control CBL sample
CBL 05--36

source_name: CBL sample 05--36


title: mESC_Trim71KO_LIF_exp1_rep1

description:
trim71_diff_timecourse_mRNA_counts.tab
sample name in processed data file:
LIF mES K