title: 9L_M_511


title: 9L_M_491

status: Public on Jul 21 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 9L_M_49


title: 9L_M_488


title: 9L_M_489


title: 9L_M_486


title: 9L_M_598


title: 9L_M_498


title: 9L_M_485


title: 9L_M_483


title: 9L_M_479


title: 9L_M_481


title: 9L_M_48


title: 9L_M_497


title: 9L_M_477


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title: 9L_M_492


title: 9L_M_475


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title: 9L_M_471


title: 9L_M_480


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title: 9L_M_487


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title: 9L_M_484


title: 9L_M_465


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title: 9L_M_467


title: 9L_M_464


title: 9L_M_462


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title: 9L_M_460


title: 9L_M_459


title: 9L_M_46


title: 9L_M_457


title: 9L_M_455


title: 9L_M_456


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title: 9L_M_452


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title: 9L_M_445


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title: 9L_M_1455


title: 9L_M_1450


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title: 9L_M_145


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title: 9L_M_1435


title: 9L_M_1443


title: 9L_M_1438


title: 9L_M_1444


title: 9L_M_1445


title: 9L_M_1436


title: 9L_M_1439


title: 9L_M_1437


title: 9L_M_144


title: 9L_M_1440


title: 9L_M_1457


title: 9L_M_1441


title: 9L_M_1433


title: 9L_M_1430


title: 9L_M_143


title: 9L_M_1431


title: 9L_M_1429


title: 9L_M_1432


title: 9L_M_1447


title: 9L_M_1425


title: 9L_M_1423


title: 9L_M_1424


title: 9L_M_1421


title: 9L_M_1422


title: 9L_M_1426


title: 9L_M_1434


title: 9L_M_1472


title: 9L_M_1418


title: 9L_M_142


title: 9L_M_1419


title: 9L_M_1415


title: 9L_M_1416


title: 9L_M_1410


title: 9L_M_141


title: 9L_M_1413


title: 9L_M_1411


title: 9L_M_1414


title: 9L_M_1409


title: 9L_M_1428


title: 9L_M_1406


title: 9L_M_1407


title: 9L_M_1408


title: 9L_M_1412


title: 9L_M_1404


title: 9L_M_1405


title: 9L_M_1427


title: 9L_M_1420


title: 9L_M_1402


title: 9L_M_1403


title: 9L_M_14


title: 9L_M_1398


title: 9L_M_1399


title: 9L_M_1417


title: 9L_M_140


title: 9L_M_1395


title: 9L_M_1394


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title: 9L_M_1390


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title: 9L_M_1384


title: 9L_M_1389


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title: 9L_M_1380


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title: 9L_M_1376


title: 9L_M_1379


title: 9L_M_1373


title: 9L_M_1372


title: 9L_M_1375


title: 9L_M_1370


title: 9L_M_139


title: 9L_M_1382


title: 9L_M_1371


title: 9L_M_1369


title: 9L_M_1368


title: 9L_M_1366


title: 9L_M_1365


title: 9L_M_137


title: 9L_M_1362


title: 9L_M_136


title: 9L_M_1363


title: 9L_M_1367


title: 9L_M_1360


title: 9L_M_1357


title: 9L_M_1358


title: 9L_M_1355


title: 9L_M_1356


title: 9L_M_1359


title: 9L_M_1354


title: 9L_M_1353


title: 9L_M_1352


title: 9L_M_1401


title: 9L_M_1374


title: 9L_M_135


title: 9L_M_1350


title: 9L_M_1351


title: 9L_M_1349


title: 9L_M_1348


title: 9L_M_1361


title: 9L_M_1344


title: 9L_M_1342


title: 9L_M_1345


title: 9L_M_1341


title: 9L_M_1346


title: 9L_M_1340


title: 9L_M_1338


title: 9L_M_1337


title: 9L_M_1343


title: 9L_M_1335


title: 9L_M_1339


title: 9L_M_134


title: 9L_M_1336


title: 9L_M_1334


title: 9L_M_1333


title: 9L_M_1332


title: 9L_M_1331


title: 9L_M_1330


title: SUPT5H_g2_91

city: Boston

first: Danya

middle: J

last: Martell-Smart

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: CRISPR colony sequencing

library_source: transcriptomic

data_processing:
nSolver Analysis Software used for extracting and normalizing Nanostring direct mRNA levels (RCC files)
Assembly: GRCh38
Supplementary files format and content: *_aln.txt and *.seq files contain the CRISPR variant detection results
Library strategy: CRISPR colony sequencing

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Qiazol extraction
Qiazol extraction

tag: tissue

value: Bone Marrow

tag: cell type

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: de-identified donor

tag: developmental stage

value: progenitors

tag: treatment

value: SUPT5H gRNA


title: SUPT5H_g1_90

description: CRISPR colony sequencing


title: SUPT5H_g2_88

description: CRISPR colony sequencing


title: 9L_M_1328


title: SUPT5H_g2_92

description: CRISPR colony sequencing


title: AAVS1_89

description: CRISPR colony sequencing


title: 9L_M_1329


title: 9L_M_1327


title: SUPT5H_g2_87

description: CRISPR colony sequencing


title: 9L_M_1326


title: SUPT5H_g2_85

description: CRISPR colony sequencing


title: SUPT5H_g2_81

description: CRISPR colony sequencing


title: 9L_M_1323


title: 9L_M_1324


title: 9L_M_1322


title: SUPT5H_g2_86

description: CRISPR colony sequencing


title: SUPT5H_g2_79

description: CRISPR colony sequencing


title: SUPT5H_g2_78

description: CRISPR colony sequencing


title: 9L_M_1320


title: 9L_M_1321


title: 9L_M_1325


title: 9L_M_133


title: SUPT5H_g2_76

description: CRISPR colony sequencing


title: SUPT5H_g2_75

description: CRISPR colony sequencing


title: 9L_M_1319


title: 9L_M_132


title: 9L_M_1318


title: SUPT5H_g2_74

description: CRISPR colony sequencing


title: SUPT5H_g2_73

description: CRISPR colony sequencing


title: 9L_M_1317


title: 9L_M_1314


title: SUPT5H_g2_82

description: CRISPR colony sequencing


title: 9L_M_1316


title: 9L_M_1315


title: 9L_M_1312


title: SUPT5H_g2_83

description: CRISPR colony sequencing


title: SUPT5H_g2_69

description: CRISPR colony sequencing


title: SUPT5H_g2_84

description: CRISPR colony sequencing


title: SUPT5H_g2_80

description: CRISPR colony sequencing


title: SUPT5H_g2_68

description: CRISPR colony sequencing


title: 9L_M_1310


title: SUPT5H_g2_66

description: CRISPR colony sequencing


title: 9L_M_1311


title: SUPT5H_g2_67

description: CRISPR colony sequencing


title: SUPT5H_g2_65

description: CRISPR colony sequencing


title: SUPT5H_g2_77

description: CRISPR colony sequencing


title: 9L_M_1308


title: 9L_M_1307


title: SUPT5H_g2_64

description: CRISPR colony sequencing


title: 9L_M_131


title: SUPT5H_g2_61

description: CRISPR colony sequencing


title: 9L_M_1305


title: SUPT5H_g2_63

description: CRISPR colony sequencing


title: 9L_M_1309


title: 9L_M_1304


title: 9L_M_1306


title: SUP5H_g2_72

description: CRISPR colony sequencing


title: 9L_M_1302


title: SUP5H_g2_71

description: CRISPR colony sequencing


title: 9L_M_1303


title: SUP5H_g2_70

description: CRISPR colony sequencing


title: SUPT5H_g2_57

description: CRISPR colony sequencing


title: 9L_M_1301


title: SUPT5H_g1_56

description: CRISPR colony sequencing


title: SUPT5H_g1_55

description: CRISPR colony sequencing


title: 9L_M_130


title: 9L_M_13


title: SUPT5H_g2_62

description: CRISPR colony sequencing


title: 9L_M_1298


title: SUPT5H_g1_54

description: CRISPR colony sequencing


title: 9L_M_1296


title: SUPT5H_g1_52

description: CRISPR colony sequencing


title: SUPT5H_g1_50

description: CRISPR colony sequencing


title: SUPT5H_g1_51

description: CRISPR colony sequencing


title: SUPT5H_g1_53

description: CRISPR colony sequencing


title: SUPT5H_g2_59

description: CRISPR colony sequencing


title: 9L_M_1292


title: SUPT5H_g2_58

description: CRISPR colony sequencing


title: 9L_M_1293


title: 9L_M_1291


title: 9L_M_1294


title: 9L_M_1290


title: SUPT5H_g1_45

description: CRISPR colony sequencing


title: 9L_M_1300


title: SUPT5H_g1_44

description: CRISPR colony sequencing


title: 9L_M_1299


title: SUPT5H_g1_43

description: CRISPR colony sequencing


title: 9L_M_1289


title: SUPT5H_g1_41

description: CRISPR colony sequencing


title: SUPT5H_g1_42

description: CRISPR colony sequencing


title: SUPT5H_g1_40

description: CRISPR colony sequencing


title: SUPT5H_g2_60

description: CRISPR colony sequencing


title: 9L_M_1288


title: SUPT5H_g1_39

description: CRISPR colony sequencing


title: 9L_M_1287


title: 9L_M_1297


title: 9L_M_1295


title: 9L_M_1284


title: SUPT5H_g1_49

description: CRISPR colony sequencing


title: 9L_M_1286


title: SUPT5H_g1_38

description: CRISPR colony sequencing


title: 9L_M_1285


title: SUPT5H_g1_46

description: CRISPR colony sequencing


title: 9L_M_1280


title: 9L_M_1282


title: SUPT5H_g1_48

description: CRISPR colony sequencing


title: SUPT5H_g1_37

description: CRISPR colony sequencing


title: 9L_M_1283


title: SUPT5H_g1_47

description: CRISPR colony sequencing


title: 9L_M_1281


title: 9L_M_129


title: 9L_M_1279


title: 9L_M_128


title: SUPT5H_g1_33

description: CRISPR colony sequencing


title: 9L_M_1278


title: SUPT5H_g1_31

description: CRISPR colony sequencing


title: SUPT5H_g1_32

description: CRISPR colony sequencing


title: SUPT5H_g1_36

description: CRISPR colony sequencing


title: SUPT5H_g1_35

description: CRISPR colony sequencing


title: 9L_M_1274


title: 9L_M_1277


title: 9L_M_1273


title: SUPT5H_g1_30

description: CRISPR colony sequencing

value: AAVS1 gRNA


title: SUPT5H_g1_29

description: CRISPR colony sequencing


title: 9L_M_1272


title: SUPT5H_g1_28

description: CRISPR colony sequencing


title: 9L_M_1271


title: SUPT5H_g1_26

description: CRISPR colony sequencing


title: 9L_M_127


title: SUPT5H_g1_25

description: CRISPR colony sequencing


title: 9L_M_1269


title: AAVS1_21

description: CRISPR colony sequencing


title: 9L_M_1270


title: 9L_M_1266


title: 9L_M_1268


title: 9L_M_1276


title: AAVS1_18

description: CRISPR colony sequencing


title: AAVS1_19

description: CRISPR colony sequencing


title: 9L_M_1264


title: AAVS1_17

description: CRISPR colony sequencing


title: AAVS1_15

description: CRISPR colony sequencing


title: AAVS1_20

description: CRISPR colony sequencing


title: 9L_M_1263


title: 9L_M_1262


title: SUPT5H_g1_34

description: CRISPR colony sequencing


title: SUPT5H_g1_27

description: CRISPR colony sequencing


title: AAVS1_16

description: CRISPR colony sequencing


title: AAVS1_23

description: CRISPR colony sequencing


title: AAVS1_24

description: CRISPR colony sequencing


title: 9L_M_126


title: 9L_M_1261


title: AAVS1_14

description: CRISPR colony sequencing


title: 9L_M_1260


title: AAVS1_13

description: CRISPR colony sequencing


title: 9L_M_1259


title: 9L_M_1267


title: AAVS1_9

description: CRISPR colony sequencing


title: AAVS1_8

description: CRISPR colony sequencing


title: 9L_M_1256


title: AAVS1_7

description: CRISPR colony sequencing


title: AAVS1_6

description: CRISPR colony sequencing


title: 9L_M_1255


title: 9L_M_1265


title: AAVS1_5

description: CRISPR colony sequencing


title: 9L_M_1252


title: AAVS1_4

description: CRISPR colony sequencing


title: 9L_M_1254


title: AAVS1_3

description: CRISPR colony sequencing


title: AAVS1_2

description: CRISPR colony sequencing


title: 9L_M_1250


title: 9L_M_1247


title: 9L_M_1248


title: 9L_M_1249


title: AAVS1_12

description: CRISPR colony sequencing


title: AAVS1_1

description: CRISPR colony sequencing


title: 9L_M_1246


title: 9L_M_1258


title: AAVS1_11

description: CRISPR colony sequencing


title: 9L_M_1244


title: AAVS1_10

description: CRISPR colony sequencing


title: AAVS1_22

description: CRISPR colony sequencing


title: 9L_M_1257


title: 9L_M_1242


title: 9L_M_1243


title: C3

city: Zhengzhou

first: Gaopeng

last: Yuan

state: Henan

address: Weilai Road Nanduan

country: China

institute: CAAS

data_processing:
IlluminaHiSeq software used for basecalling.
The original sequencing data contain reads with low quality, joint contamination and high unknown base N content, which should be removed before data analysis to ensure the reliability of the results.
gene expression levels were calculated by FPKM (fragments per kilobase million)
Genome_build: 97103
Supplementary_files_format_and_content: Processed data
Genome_build: Watermelon (97103) v2 Genome http://cucurbitgenomics.org/organism/1

organism: Citrullus lanatus

source_name: Watermelon

growth_protocol: Floral buds and flowers were harvested from the progeny of the watermelon variety Xinteda Zhengkang 9. The plants were grown in a greenhouse located in Henan Province, China. Floral buds were collected from 7:00 to 10:00 am and from 3:30 to 6:30 pm every day during flowering. The flower buds were placed in a 50 mL centrifuge tube and stored in 4°C until cytological observation and RNA extraction.

extract_protocol:
The remaining 2/3 of each anther was quickly stripped and submerged in liquid nitrogen and returned to the -80 °C freezer until RNA extraction. RNA was extracted using the TIANGEN kit.
RNA libraries were prepared for sequencing using standard IlluminaHiSeq

treatment_protocol: After the anther was stripped, the whole anther was divided into two parts, and 1/3 of the material was used to determine the developmental stage. After microscopic examination, each anther was classified as tetrad, mononuclear, dikaryophase, or mature stage, which were designated as A, B, C, and D, respectively. Three groups of samples were collected for each stage, for a total of 12 samples.

value: flower

value: dikaryophase


title: C2


title: 9L_M_1241


title: 9L_M_1240


title: D1

value: mature


title: C1


title: 9L_M_1239


title: 9L_M_1251


title: 9L_M_1237


title: B3

value: mononuclear


title: D3


title: D2


title: 9L_M_1245


title: B1


title: B2


title: 9L_M_1236


title: A2

value: tetrad


title: 9L_M_1235


title: 9L_M_1234


title: A3


title: 9L_M_1232


title: 9L_M_1231


title: 9L_M_123


title: 9L_M_1230


title: 9L_M_1233


title: CT29, EVT, rep1

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

data_processing:
Contact maps for each sample were generated using the Arima Genomics fragment map file specific to GRCh38 and default parameters in Juicer.
After merging contact maps for each cell state, stem and EVT, chromatin loops were discovered with HiCCUPS (Juicer Tools Version 1.22.01) using a matrix size of 1000 (-m 1000) at 5kb, 10 kb, and 25 kb resolution (-r 25000,10000,5000). Differential loops between EVT and stem were identified using HiCCUPSDiff (Juicer Tools Version 1.22.01) with a matrix size of 1000 (-m 1000). The chromatin loops as well as the differential loops were filtered to exclude contacts in the ENCODE blacklisted regions using Bedtools intersect (with option `-v`; Version 2.30.0;74).
Assembly: GRCh38.86
Supplementary files format and content: binary file containing HiC contact matrices

source_name: human trophoblast stem cells

growth_protocol: Human TS cells (Okae et al. 2018) were cultured in 100 mm tissue culture dishes coated with 5 μg/mL collagen IV (CB40233, Thermo-Fisher, Waltham, MA). Human TS cells were maintained in Complete human TS cell medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) fetal bovine serum (FBS), 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 1.5 μg/mL L-ascorbic acid (A8960, Sigma-Aldrich, St. Louis, MO), 50 ng/mL epidermal growth factor (EGF, E9644, Sigma-Aldrich), 2 μM CHIR99021 (04-0004, Reprocell, Beltsville, MD), 0.5 μM A83-01 (04-0014, Reprocell), 1 μM SB431542 (04-0010, Reprocell), 0.8 mM valproic acid (P4543, Sigma-Aldrich), and 5 μM Y27632 (04-0012-02, Reprocell). EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium [DMEM/F12 (11320033, Thermo-Fisher), 100 μm 2-mercaptoethanol, 0.2% (vol/vol) FBS, 50 μM penicillin, 50 U/mL streptomycin, 0.3% bovine serum albumin (BP9704100, Thermo-Fisher), 1% Insulin-Transferrin-Selenium-Ethanolamine solution (vol/vol, Thermo-Fisher)], 100 ng/mL of neuregulin 1 (NRG1, 5218SC, Cell Signaling, Danvers, MA), 7.5 μM A83-01 (04-0014, Reprocell, Beltsville, MD), 2.5 μM Y27632 (04-0012, Reprocell), 4% KnockOut Serum Replacement (KSR, 10828028, Thermo-Fisher), and 2% Matrigel® (CB-40234, Thermo-Fisher). On day 3 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and with a reduced Matrigel® concentration of 0.5%. On culture day 6 of EVT cell differentiation, the medium was replaced with EVT Differentiation Medium excluding NRG1 and KSR, and with a Matrigel concentration of 0.5%. Cells were analyzed on day 8 of EVT cell differentiation.

extract_protocol: Cells were rinsed with 5 mL of PBS and then 5 mL PBS containing 2% formaldehyde were added and incubated for 10 min. Then, 550 μL of glycine 1.25 M (final conc 0.125M) were added and incubated for 5 min at room temperature before an additional 15 min incubation on ice. Liquid was removed and cells were rinsed two times with 5 mL ice-cold PBS. Cells were scraped and transferred into 2 mL low bind tubes to have the equivalent of 1*10^6 cells (1 Petri Dish). Nuclei were pelleted at 2,500 rpm for 10 min at 4˚C (repeat if necessary) and all supernatant was removed, and flash frozen on dry ice and stored at -80˚C until ready for use. Crosslinked samples were thawed on ice and prepared for Hi-C using the Arima-HiC kit (Arima Genomics, San Diego, CA). Cross-linking was performed according to the Arima-HiC protocol with the following modifications. At step 5, the incubation at 37°C was increased to a duration of 60 min and the samples were maintained overnight at 4°C after step 11. Samples were then cleaned with AMPure XP Beads as described in the protocol and all quantification and quality control steps that required the use of a Qubit were performed using a Qubit dsDNA HS Assay Kit. Proximally ligated DNA (1000 ng/sample) was used as an input into the library preparation protocol. Samples were sheared to 400 bp using a Covaris LE220-plus system using the manufacturer’s recommended settings. Sizing was confirmed using a High Sensitivity DNA Bioanalyzer kit. Size-selection as described in the Arima-HiC protocol was followed and the entire size-selected sample was used as input into biotin enrichment and library preparation with a KAPA HyperPrep kit and Roche SeqCap Adapters (7141530001 or 7141548001, Roche). Instead of performing the Arima-HiC quality control step 2, the number of cycles needed for library amplification was determined as follows: perform 10 PCR cycles for 125-200 ng of input, perform 9 PCR cycles for 200-400 ng of input, perform 8 PCR cycles for 400-600 ng of input, and perform 7 cycles of PCR for inputs greater than 600 ng. The completed libraries were then quantified using a Qubit dsDNA BR Assay Kit and the library size was determined with a High Sensitivity DNA Bioanalyzer Kit. Standard Illumina Free-Adapter Blocking was performed on the libraries. Cleaned, adapter-blocked libraries were loaded on a NovaSeq6000 with a run configuration of 151x8x8x151 and an average depth of 900M PE reads per library.

value: human trophoblast stem cells

tag: cell line

value: extravillous trophoblast cell


title: CT27, EVT, rep2


title: CT27, EVT, rep1


title: CT27, EVT, rep3


title: CT29, EVT, rep3


title: CT29, EVT, rep2


title: 9L_M_1228


title: CT29, Stem, rep1

value: stem state trophoblast cell


title: CT27, Stem, rep3


title: CT29, Stem, rep2


title: 9L_M_1221


title: CT27, Stem, rep1


title: 9L_M_1238


title: A1


title: 9L_M_1224


title: CT27, Stem, rep2


title: 9L_M_1220


title: 9L_M_1222


title: 9L_M_1225


title: 9L_M_122


title: 9L_M_1223


title: 9L_M_1226


title: CT29, Stem, rep3


title: 9L_M_1219


title: 9L_M_1217


title: 9L_M_1218


title: 9L_M_1216


title: ChIP_HEK293T_Input_1 human

city: Orange

first: Matthew

last: Simon

state: CT

address: 100 West Campus Drive, Ste MIC 231

department: Molecular Biophysics and Biochemistry

institute: Yale University

description:
ChIP Input DNA
Input DNA was aligned to human genome and used as reference for generation of FE bigWig files.

data_processing:
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For ChIP-seq, reads were aligned to the BDGP6 or GRCh38 genome using Bowtie2 aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
Peaks were called using MACS2 with default parameters for narrow peak calling.
Fold enrichment tracks were created using MACS2 bdgcamp function using input as the comparison.
Assembly: BDGP6 or GRCh38

source_name: HEK293T cells

growth_protocol: HEK-293T cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. S2 cells were cultured at 27°C in Schneider's Drosophila Medium with 10% heat-inactivated FBS and 1% Penicillin/Streptomycin.

extract_protocol:
HEK293T cells were washed twice with PBS and crosslinked with 1% formaldehyde (Pierce) for 10 min at room temperature. Crosslinking was quenched with 125 mM (final) glycine for 5 min and washed twice with PBS. Cells were lysed in 4 ml lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), 1x Protease inhibitor (Roche) for 10 min on ice. Lysed cells were centrifuged at 4,000 rpm for 5 min at 4°C and washed twice with 4 ml cold wash buffer (10 mM Tris-Cl pH 7.5, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0), 1x protease inhibitors. The pellet was resuspended in 1 ml shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris pH 7.5), 1x protease inhibitor and sheared on Covaris S220 (140 W, 5% duty factor, 200 bursts per cycle, 4°C) for 12 min (determined by time course optimization experiment). Extract was diluted with Triton X-100 (1% final) and NaCl (150 mM final) and cleared by centrifugation at 21,000g, 4°C for 10 min. For input, 10% of material was set aside. Cleared extract was supplemented with 2 μL of antibody and 100 nM competitor peptide and incubated overnight at 4°C. Immuno-precipitated chromatin was captured on 30 μl of Dynabeads protein G (Invitrogen) at 4°C for 1.5 hours. Beads were washed twice with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 150 mM NaCl), twice with high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 500 mM NaCl), once with LiCl Buffer (100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Enriched DNA was eluted in 100 μl of proteinase K buffer (20mM HEPES pH 7.5, 1 mM EDTA, 0.5% SDS) supplemented with 40 μg of proteinase K (Ambion) for 30 min at 50°C. Formaldehyde crosslinks were reversed by adding NaCl (150 mM final) and 0.25 μg DNase-free RNase (Roche), followed by incubation overnight at 65°C. DNA was isolated using QIAquick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared based on a protocol adapted from Bowman et al., BMC Genomics 2013. DNA ends were first polished in a reaction containing NEB T4 Ligase Buffer, NEB T4 PNK, NEB T4 DNA Polymerase, and NEB Klenow DNA Polymerase. After minElute PCR purification (Quiagen), A-tailing was performed using NEB buffer #2 and NEB Klenow 3'-5' exo minus. Adapter ligations were performed using the NEB Blunt/TA Ligase Mastermix and 1 uM mPE Universal Adapters (A.U1 + A.U2). Libraries were amplified and indexed by PCR amplification using 2x Phusion Mastermix, PCR.U universal primer, and PCR.X indexing primers (6-10 cycles).  Indexed libraries were then cleaned by 1.5x SPRI bead purification.

treatment_protocol: For ChIP-seq, HEK293T cells were left untreated.

value: WT HEK293T

tag: s4u feed

value: No


title: ChIP_HEK293T_H4Kacme_H4Kaccomp_2

description:
ChIP Enriched DNA
MACS2 was used for narrow peak calling of aligned ChIP-seq reads


title: 9L_M_1215


title: ChIP_HEK293T_H4Kacme_nocomp_2


title: ChIP_HEK293T_H4Kacme_H4Kacmecomp_2


title: TT-TL_HEK293T_DMSO_1

description:
Nascent RNA
Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For TT-TL-seq, reads were aligned to the GRCh38 genome using HISAT-3N aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Tracks were converted to binary format using IGVtools (toTDF).
Assembly: BDGP6 or GRCh38

extract_protocol:
For TT-TL-seq, RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. Genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. 50 μg of total RNA was subjected to MTS chemistry, followed by biotinylation and streptavidin enrichment as previously described (Duffy et al., 2015). Nascent enriched RNA for TT-TimeLapse-seq RNA was then treated with oxidative-nucleophilic-aromatic-substitution chemistry using mCPBA as the oxidant as previously described (Schofield et al., Nature Methods 2018).
TT-TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: For TT-TL-seq, HEK293T cells were treated with 400nM TSA or DMSO for 15 hours, and 1 mM s4U for the last 5 minutes of TSA/DMSO treatment.

value: Yes (1mM, 5 minutes)


title: TT-TL_HEK293T_TSA_2

data_processing:
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For TT-TL-seq, reads were aligned to the GRCh38 genome using HISAT-3N aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
T-to-C mutations were identified using Rsamtools and a custom R script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
To examine the distribution of reads with each minimum number of T-to-C mutations, bam files were filtered using Picard tools.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType bedGraph).
Assembly: BDGP6 or GRCh38


title: TT-TL_HEK293T_TSA_1


title: TT-TL_HEK293T_DMSO_2


title: 9L_M_1212


title: 9L_M_1213


title: 9L_M_1210


title: ChIP_HEK293T_H4Kacme_H4Kacmecomp_1


title: 9L_M_1209


title: ChIP_HEK293T_H4Kacme_H4Kprcomp_1


title: ChIP_HEK293T_H4Kacme_H4Kaccomp_1


title: 9L_M_1207


title: ChIP_HEK293T_H4Kacme_nocomp_1


title: 9L_M_1208


title: 9L_M_1205


title: ChIP_HEK293T_panKacme_H4Kaccomp_3

extract_protocol:
HEK293T cells were washed twice with PBS and crosslinked with 1% formaldehyde (Pierce) for 10 min at room temperature. Crosslinking was quenched with 125 mM (final) glycine for 5 min and washed twice with PBS. Cells were lysed in 4 ml lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), 1x Protease inhibitor (Roche) for 10 min on ice. Lysed cells were centrifuged at 4,000 rpm for 5 min at 4°C and washed twice with 4 ml cold wash buffer (10 mM Tris-Cl pH 7.5, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0), 1x protease inhibitors. The pellet was resuspended in 1 ml shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris pH 7.5), 1x protease inhibitor and sheared on Covaris S220 (140 W, 5% duty factor, 200 bursts per cycle, 4°C) for 12 min (determined by time course optimization experiment). Extract was diluted with Triton X-100 (1% final) and NaCl (150 mM final) and cleared by centrifugation at 21,000g, 4°C for 10 min. For input, 10% of material was set aside. Cleared extract was supplemented with 2 μL of antibody and 75 nM competitor peptide and incubated overnight at 4°C. Immuno-precipitated chromatin was captured on 30 μl of Dynabeads protein G (Invitrogen) at 4°C for 1.5 hours. Beads were washed twice with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 150 mM NaCl), twice with high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 500 mM NaCl), once with LiCl Buffer (100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Enriched DNA was eluted in 100 μl of proteinase K buffer (20mM HEPES pH 7.5, 1 mM EDTA, 0.5% SDS) supplemented with 40 μg of proteinase K (Ambion) for 30 min at 50°C. Formaldehyde crosslinks were reversed by adding NaCl (150 mM final) and 0.25 μg DNase-free RNase (Roche), followed by incubation overnight at 65°C. DNA was isolated using QIAquick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared by the Yale Center for Genome Analysis.


title: ChIP_HEK293T_panKacme_H4Kprcomp_3


title: ChIP_HEK293T_panKacme_H4Kacmecomp_3


title: 9L_M_1204


title: 9L_M_1203


title: ChIP_HEK293T_H4Kacme_H4Kprcomp_2


title: 9L_M_1214


title: ChIP_HEK293T_panKacme_H4Kprcomp_2


title: ChIP_HEK293T_panKacme_nocomp_3


title: ChIP_HEK293T_panKacme_H4Kacmecomp_2


title: 9L_M_1202


title: 9L_M_120


title: 9L_M_1200


title: 9L_M_1201


title: 9L_M_12


title: 9L_M_1199


title: 9L_M_1206


title: 9L_M_1198


title: ChIP_HEK293T_panKacme_H4Kprcomp_1


title: ChIP_HEK293T_panKacme_H4Kaccomp_1


title: ChIP_HEK293T_panKacme_H4Kacmecomp_1


title: 9L_M_1197


title: ChIP_HEK293T_panKacme_nocomp_1


title: ChIP_HEK293T_H4Kacme_2

description: MACS2 was used for narrow peak calling of aligned ChIP-seq reads

data_processing:
Reads were trimmed using cutadapt (--minimum-length=20)
Reads were filtered for unique sequences using FastUniq
Reads were trimmed using cutadapt (--minimum-length=20)
For ChIP-seq, reads were aligned to the GRCh38 genome using Bowtie2 aligned with default parameters.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely (flag: 83/163, 99/147), with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode)
Peaks were called using MACS2 with default parameters for narrow peak calling.
Fold enrichment tracks were created using MACS2 bdgcamp function using input as the comparison.
Assembly: GRCh38

growth_protocol: HEK-293T cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
HEK293T cells were washed twice with PBS and crosslinked with 1% formaldehyde (Pierce) for 10 min at room temperature. Crosslinking was quenched with 125 mM (final) glycine for 5 min and washed twice with PBS. Cells were lysed in 4 ml lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), 1x Protease inhibitor (Roche) for 10 min on ice. Lysed cells were centrifuged at 4,000 rpm for 5 min at 4°C and washed twice with 4 ml cold wash buffer (10 mM Tris-Cl pH 7.5, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0), 1x protease inhibitors. The pellet was resuspended in 1 ml shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris pH 7.5), 1x protease inhibitor and sheared on Covaris S220 (140 W, 5% duty factor, 200 bursts per cycle, 4°C) for 12 min (determined by time course optimization experiment). Extract was diluted with Triton X-100 (1% final) and NaCl (150 mM final) and cleared by centrifugation at 21,000g, 4°C for 10 min. For input, 10% of material was set aside. Cleared extract was supplemented with 2 μg of antibody and incubated overnight at 4°C. Immuno-precipitated chromatin was captured on 30 μl of Dynabeads protein G (Invitrogen) at 4°C for 1.5 hours. Beads were washed twice with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 150 mM NaCl), twice with high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 500 mM NaCl), once with LiCl Buffer (100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Enriched DNA was eluted in 100 μl of proteinase K buffer (20mM HEPES pH 7.5, 1 mM EDTA, 0.5% SDS) supplemented with 40 μg of proteinase K (Ambion) for 30 min at 50°C. Formaldehyde crosslinks were reversed by adding NaCl (150 mM final) and 0.25 μg DNase-free RNase (Roche), followed by incubation overnight at 65°C. DNA was isolated using QIAquick PCR purification kit (QIAGEN)
ChIP-seq libraries were prepared based on a protocol adapted from Bowman et al., BMC Genomics 2013. DNA ends were first polished in a reaction containing NEB T4 Ligase Buffer, NEB T4 PNK, NEB T4 DNA Polymerase, and NEB Klenow DNA Polymerase. After minElute PCR purification (Qiagen), A-tailing was performed using NEB buffer #2 and NEB Klenow 3'-5' exo minus. Adapter ligations were performed using the NEB Blunt/TA Ligase Mastermix and 1 uM mPE Universal Adapters (A.U1 + A.U2). Libraries were amplified and indexed by PCR amplification using 2x Phusion Mastermix, PCR.U universal primer, and PCR.X indexing primers (6-10 cycles).  Indexed libraries were then cleaned by 1.5x SPRI bead purification.


title: 9L_M_1196


title: 9L_M_1195


title: ChIP_HEK293T_H4Kacme_1


title: 9L_M_1194


title: ChIP_HEK293T_Kacme_2


title: 9L_M_1193


title: ChIP_HEK293T_Kacme_1


title: 9L_M_1190


title: 9L_M_1191


title: 9L_M_1192


title: ChIP_HEK293T_panKacme_nocomp_2


title: ChIP_HEK293T_Input_1


title: ChIP_HEK293T_Input_2


title: ChIP_HEK293T_panKacme_H4Kaccomp_2


title: ChIP_HEK293T_Input_3


title: 9L_M_1187


title: 9L_M_1189


title: ECFC_92n4b

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between donors.
Assembly: hg19
Supplementary files format and content: .gene.mmseq files contain counts per gene

source_name: Human Umbilical Cord Blood

growth_protocol: Mononuclear cells were isolated from umbilical cord blood via density gradient centrifugation. Cultured in Endothelial Cell Growth Medium MV Kit (PromoCell), ECFC grew out after few days and were further expanded.

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA/miRNA Kit (Qiagen) according to the manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300 ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

treatment_protocol: Baseline (PromoCell media)

tag: individual

value: Donor 57

value: endothelial progenitor cell

tag: group

value: overweight

tag: Sex

value: male


title: ECFC_97n4b

value: Donor 60


title: ECFC_96n4b

value: Donor 59


title: ECFC_58n4b

value: Donor 53


title: ECFC_54n5b

value: Donor 52


title: 9L_M_1184


title: 9L_M_1183


title: ECFC_44n4b

value: Donor 51


title: 9L_M_119


title: ECFC_95n4b

value: Donor 58


title: 9L_M_1188


title: ECFC_73n5b

value: Donor 56


title: 9L_M_1186


title: 9L_M_1180


title: ECFC_98n4b

value: Donor 49

value: female


title: 9L_M_118


title: ECFC_82n4b

value: Donor 47


title: ECFC_65n5b

value: Donor 55


title: slr1- polysome RNA, biol repl 2

city: Toronto

first: Farnaz

last: Mansouri-Noori

state: ON

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

description: SE 50bp reads

data_processing:
Sequencing was performed by The Centre for Applied Genomics (TCAG, Toronto, Canada).
Alignment and quantitation of FASTQ files was performed using RSEM/Bowtie.
Differential translation analysis was performed by utilizing the R Babel framework as described in Olshen et al., Bioinformatics, 2013.
Assembly: Schizosaccharomyces pombe(972h-)
Supplementary files format and content: Tab delimited text file includes raw counts for each sample.

organism: Schizosaccharomyces pombe

growth_protocol: YES medium, 32°C, 200 rpm

extract_protocol:
TRIzol RNA extraction was performed on total RNA and polysome RNA samples for two biological replicates prior to library preparation and sequencing.
Ribo-Zero Gold rRNA Removal Kit (Yeast, Illumina) was used followed by library preparation using TruSeq Stranded Total RNA Kit (Illumina) according to manufacturer's protocol.

treatment_protocol: 100 µg/mL cycloheximide

value: fission yeast

tag: genotype

value: KO

value: 100 µg/mL cycloheximide


title: 9L_M_1185


title: slr1- polysome RNA, biol repl 1

description: SE 50bp reads


title: slr1- total RNA, biol repl 2

description: SE 50bp reads


title: 9L_M_1182


title: 9L_M_1181


title: 9L_M_1177


title: ECFC_74n5b

value: Donor 45

value: endothelial progenitor cell


title: slr1- total RNA, biol repl 1

description: SE 50bp reads


title: ECFC_99n4b

value: Donor 50

value: overweight


title: 9L_M_1179


title: WT polysome RNA, biol repl 2

description: SE 50bp reads

value: WT


title: 9L_M_1178


title: ECFC_87n4b

value: Donor 48


title: ECFC_79n4b

value: Donor 46


title: ECFC_59n4b

value: Donor 54

value: male


title: ECFC_67n4b

value: Donor 44


title: WT polysome RNA, biol repl 1

description: SE 50bp reads


title: 9L_M_1176


title: WT total RNA, biol repl 2

description: SE 50bp reads


title: ECFC_62n4b

value: Donor 43


title: 9L_M_1175


title: GSC272 cells, shTFPI2 rep2

city: Cleveland

first: Lizhi

last: Pang

state: OH

address: 9500 Euclid Avenue

department: Department of Cancer Biology

institute: Cleveland Clinic

data_processing:
Galaxy server
Trimmomatic was performed to read and trim paired-end reads.
HISAT2 program was used to align the data where hg38 was selected as the reference genome.
Samtools merge was performed on BAM files to merge data from different flowcells.
Gene expression was then determined by FeatureCounts.
Limma was used to calculate differential expression genes and generate DE table.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: GSC272 cells were maintained in neural stem cell (NSC) proliferation media (Millipore, #SCM005) containing 20 ng/ml epidermal growth factor (EGF; PeproTech, #AF-100-15) and basic fibroblast growth factor (bFGF; PeproTech, #100-18B) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared at The University of Chicago Functional Genomics (RRID:SCR_019196).

treatment_protocol: Cells were transfected with shC or shTFPI2 plasmid using lentiviral particles.

value: Glioma stem cells

value: TFPI2 knockdown

tag: time

value: Day 0


title: ECFC_51n4b

value: Donor 42

value: female


title: 9L_M_1174


title: GSC272 cells, shTFPI2 rep1


title: ECFC_48n4b

value: Donor 41


title: shControl_2

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Single-end 50-bp sequenced reads were analyzed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v.0.10.1. Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 using Bowtie v.1.0.0 and SAMtools v.0.1.1.9, allowing two mismatches and 20 multihits. Differential expression was calculated with Cufflinks v.2.2.1 using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml. GSEAPreranked was used to perform GSEA of the described gene signatures on a pre-ranked gene list, setting 1,000 gene set permutations.
Assembly: GRCh37
Supplementary files format and content: Normalized counts obtained with Cuffnorm (Cufflinks)

molecule: polyA RNA

source_name: STS26T cells expressing scramble shRNA

growth_protocol: STS26T MPNST cells were maintained in high glucose Dulbecco's modified Eagles's medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 1mM sodium piruvate and 20 µg/ml gentamicin at 37ºC in a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen). After the recovery of the aqueous phase using chlorophorm, a DNAse treatment was performed using the Mini RNeasy kit (Qiagen) following manufacturer instructions.  cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit, and sequenced on a Illumina HiSeq2500 sequencer.
Total RNA from tissues or cells was extracted using the TRIZOL Reagent (Invitrogen). After recovery of the aqueous phase using chloroform, DNase treatment and further purification were performed using the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions.  RNA sequencing (RNA-seq) was conducted by the CNIO Genomics Unit. Total RNA (1 µg) from samples was used. The average sample RNA Integrity Number was 9.65 (Agilent 2100 Bioanalyzer). cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on an Illumina HiSeq 2500 sequencer.

treatment_protocol: STS26T cells were transduced with the lentiviruses at a multiplicity of infection (MOI) of 10 in the presence of 8 μg/ml polybrene. Selection of infected cells was started 48 hours after infection with 1 μg/ml puromycin

value: MPNST cell line (ATCC)

value: Lentiviral particles encoding scramble shRNA


title: 9L_M_1173


title: ECFC_40d3b

value: Donor 40

value: endothelial progenitor cell

value: gestational diabetes


title: shENG_1

source_name: STS26T cells expressing ENG shRNA

value: Lentiviral particles encoding ENG shRNA


title: shControl_1


title: 9L_M_1172


title: shENG_2


title: ECFC_39d4b

value: Donor 39


title: GSC272 cells, shControl rep2

value: WT


title: ECFC_36d4b

value: Donor 38

value: male


title: 9L_M_117


title: 9L_M_1168


title: 9L_M_1169


title: WT total RNA, biol repl 1

description: SE 50bp reads

value: fission yeast

value: 100 µg/mL cycloheximide


title: CBX, PBS, Day 5, Rep 3

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/VEEV_TC-83 concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with VEEV TC-83 lab reference genome
Supplementary files format and content: tab-delimited text files include total counts for each sample
Supplementary files format and content: tab-delimited text files include total counts, TPM, CPM, and RPKM values for each sample

source_name: Brain

extract_protocol:
Total RNA was isolated using MagMAX  mirVana Total RNA Isolation Kit on a KingFisher Flex instrument
Libraries were constructed using NEB NEBNext Ultra II RNA Kits

value: Brain

value: cerebellum

tag: timepoint(dpi)

value: Day 5

value: Mock


title: CBX, PBS, Day 5, Rep 1


title: CBX, PBS, Day 5, Rep 2


title: CBX, PBS, Day 5, Rep 4


title: ECFC_33d5b

value: Donor 37


title: 9L_M_1165


title: CBX, PBS, Day 1, Rep 3

value: Day 1


title: CBX, PBS, Day 1, Rep 4


title: ECFC_30d4b

value: Donor 36


title: THA, PBS, Day 5, Rep 4

value: thalamus


title: 9L_M_1164


title: ECFC_28d4b

value: Donor 34

value: endothelial progenitor cell


title: ECFC_29d4b

value: Donor 35

value: gestational diabetes


title: 9L_M_1162


title: 9L_M_1163


title: GSC272 cells, shControl rep1

value: Glioma stem cells

value: WT

value: Day 0


title: CBX, PBS, Day 1, Rep 2


title: THA, PBS, Day 5, Rep 1


title: ECFC_25d4b

value: Donor 33

value: male


title: THA, PBS, Day 1, Rep 4

value: Brain


title: 9L_M_1161


title: THA, PBS, Day 1, Rep 3


title: CBX, PBS, Day 1, Rep 1

value: cerebellum


title: THA, PBS, Day 5, Rep 2

value: Day 5


title: ECFC_22d4b

value: Donor 32


title: ECFC_12d4b

value: Donor 31


title: 9L_M_1160


title: ECFC_34d5b

value: Donor 30

value: female


title: 9L_M_1159


title: STX, PBS, Day 5, Rep 2

value: sensory cortex

value: Mock


title: STX, PBS, Day 5, Rep 4


title: THA, PBS, Day 1, Rep 1

value: thalamus

value: Day 1


title: THA, PBS, Day 1, Rep 2


title: ECFC_27d4b

value: Donor 29

value: endothelial progenitor cell

value: gestational diabetes


title: STX, PBS, Day 5, Rep 3


title: STX, PBS, Day 5, Rep 1


title: STX, PBS, Day 1, Rep 4


title: THA, PBS, Day 5, Rep 3


title: 9L_M_1156


title: STX, PBS, Day 1, Rep 3


title: STX, PBS, Day 1, Rep 1


title: HIP, PBS, Day 5, Rep 2

value: hippocampus


title: ECFC_26d4b

value: Donor 28


title: STX, PBS, Day 1, Rep 2


title: HIP, PBS, Day 5, Rep 3


title: HIP, PBS, Day 5, Rep 1


title: 9L_M_1158


title: ECFC_17d4b

value: Donor 26


title: ECFC_16d4b

value: Donor 25


title: ECFC_20d4b

value: Donor 27


title: 9L_M_1154


title: HIP, PBS, Day 5, Rep 4

value: Brain

value: Day 5


title: HIP, PBS, Day 1, Rep 4


title: 9L_M_1153


title: HIP, PBS, Day 1, Rep 3


title: 9L_M_1157


title: HIP, PBS, Day 1, Rep 1


title: MTX, PBS, Day 5, Rep 4

value: motor cortex


title: HIP, PBS, Day 1, Rep 2


title: 9L_M_1151


title: ECFC_10d4b

value: Donor 23


title: 9L_M_1152


title: 9L_M_1155


title: MTX, PBS, Day 5, Rep 2


title: 9L_M_1150


title: ECFC_09d4b

value: Donor 22

value: female


title: ECFC_08d4b

value: Donor 21


title: ECFC_15d4b

value: Donor 24


title: MTX, PBS, Day 5, Rep 1

value: Mock


title: MTX, PBS, Day 1, Rep 4

value: Day 1


title: MTX, PBS, Day 1, Rep 3


title: MTX, PBS, Day 1, Rep 2


title: ECFC_69n4b

value: Donor 19

value: endothelial progenitor cell

value: lean

value: male


title: MTX, PBS, Day 1, Rep 1


title: STR, PBS, Day 5, Rep 4

value: striatum


title: 9L_M_1149


title: 9L_M_1148


title: ECFC_41n4b

value: Donor 18


title: STR, PBS, Day 5, Rep 3


title: STR, PBS, Day 5, Rep 2


title: 9L_M_1147


title: STR, PBS, Day 5, Rep 1


title: ECFC_40n4b

value: Donor 17


title: MTX, PBS, Day 5, Rep 3

value: Brain


title: 9L_M_1146


title: STR, PBS, Day 1, Rep 3


title: STR, PBS, Day 1, Rep 1


title: 9L_M_1143


title: ECFC_39n4b

value: Donor 16


title: 9L_M_1144


title: PIR, PBS, Day 5, Rep 4

value: piriform cortex

value: Day 5


title: STR, PBS, Day 1, Rep 2


title: 9L_M_1142


title: ECFC_31n4b

value: Donor 15


title: 9L_M_115


title: ECFC_90n4b

value: Donor 20


title: 9L_M_1145


title: 9L_M_1141


title: ECFC_20n4b

value: Donor 12


title: ECFC_28n4b

value: Donor 13


title: PIR, PBS, Day 1, Rep 2

value: Mock


title: PIR, PBS, Day 5, Rep 3


title: PIR, PBS, Day 1, Rep 3

value: Day 1


title: PIR, PBS, Day 1, Rep 4


title: MOB, PBS, Day 5, Rep 4

value: main olfactory bulb


title: PIR, PBS, Day 1, Rep 1


title: 9L_M_1140


title: PIR, PBS, Day 5, Rep 1


title: MOB, PBS, Day 5, Rep 3


title: STR, PBS, Day 1, Rep 4


title: ECFC_66n4b

value: Donor 10

value: endothelial progenitor cell

value: female


title: ECFC_11n4b

value: Donor 11

value: lean

value: male


title: PIR, PBS, Day 5, Rep 2

value: Brain


title: ECFC_30n5b

value: Donor 14


title: 9L_M_114


title: MOB, PBS, Day 5, Rep 1


title: MOB, PBS, Day 1, Rep 3


title: ECFC_47n4b

value: Donor 9


title: MOB, PBS, Day 1, Rep 4


title: ECFC_45n4b

value: Donor 8


title: 9L_M_1138


title: MOB, PBS, Day 1, Rep 2


title: 9L_M_1139


title: MOB, PBS, Day 1, Rep 1


title: CBX, Virus, Day 7, Rep 4

value: cerebellum

value: Day 7

value: Infected with VEEV-TC


title: CBX, Virus, Day 7, Rep 2


title: CBX, Virus, Day 7, Rep 1


title: 9L_M_1137


title: ECFC_29n4b

value: Donor 7


title: ECFC_18n5b

value: Donor 5


title: 9L_M_1136


title: CBX, Virus, Day 6, Rep 4

value: Day 6


title: MOB, PBS, Day 5, Rep 2

value: main olfactory bulb

value: Day 5

value: Mock


title: 9L_M_1135


title: 9L_M_1134


title: ECFC_22n5b

value: Donor 6

value: endothelial progenitor cell

value: female


title: CBX, Virus, Day 6, Rep 3


title: CBX, Virus, Day 6, Rep 1


title: CBX, Virus, Day 6, Rep 2


title: CBX, Virus, Day 5, Rep 4


title: 9L_M_1133


title: CBX, Virus, Day 5, Rep 3


title: CBX, Virus, Day 7, Rep 3


title: CBX, Virus, Day 5, Rep 2


title: ECFC_12n4b

value: Donor 2

value: lean


title: ECFC_09n6b

value: Donor 1


title: 9L_M_1132


title: CBX, Virus, Day 5, Rep 1

value: Brain


title: CBX, Virus, Day 3, Rep 3

value: Day 3


title: 9L_M_1131


title: ECFC_17n4b

value: Donor 4


title: ECFC_13n4b

value: Donor 3


title: 9L_M_113


title: 9L_M_1130


title: CBX, Virus, Day 1, Rep 4

value: cerebellum

value: Day 1

value: Infected with VEEV-TC


title: THA, Virus, Day 7, Rep 4

value: thalamus

value: Day 7


title: TTTL_293T_2

description: Reads filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos)

data_processing:
STL-seq data was treated as single-end sequencing data using only read 1 (R1).
Reads were filtered for unique sequences using FastUniq (this step excluded for STL-seq).
Reads were trimmed using cutadapt (--minimum-length=20).
For TT-TL-seq, reads were aligned to the GRCh38 genome using HISAT-3N aligned with default parameters. For STL-seq reads were aligned to the GRCh38 genome with Bismark and Bowtie2 with default parameters and --local.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely, with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode).
T-to-C mutations were identified using a custom script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType tdf), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
For STL-seq, TSSs and their associated genes were identified by combining all bam files and analyzing them with TSScall with default parameters.
Half-life estimates from STL-seq data were estimated using an R package, bakR.
Assembly: GRCh38
Supplementary files format and content: Processed data files include tdf files to visualize sequencing data in IGV, a table of read counts by gene from TT-TL-seq, and a table of read counts, promoter-proximal pausing first-rder rate constants, and rate constant standard deviations from STL-seq.

source_name: Human embryonic kidnery 293T cells

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). S2 cells were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml). 293T cell cultures were maintained at 37℃.

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TT-TL-seq genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TT-TL-seq RNA was enriched with MTS-biotin and treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. For STL-seq, total RNA was treated with oxidative-nucleophilic-aromatic-substitution chemistryusing mCPBA as the oxidant and short capped RNA was enriched as described in Zimmer et al. Mol Cell 2021.
TT-TL-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). STL-seq libraries were generated with custom oligos following methods described in Zimmer et al. Mol Cell 2021.

treatment_protocol: 293T cells were treated with 1mM s4U for 5 minutes or untreated as unlabeled controls.

value: Human embryonic kidnery 293T cells

value: WT

value: Yes

tag: molecule subtype

value: s4U nascent RNA


title: CBX, Virus, Day 1, Rep 2

tag: brain region


title: CBX, Virus, Day 3, Rep 1


title: 9L_M_1129

tag: age


title: CBX, Virus, Day 1, Rep 3


title: CBX, Virus, Day 1, Rep 1


title: 9L_M_1128

tag: strain


title: THA, Virus, Day 7, Rep 3

tag: tissue


title: RNAseq_293T_unlab

tag: cell type

value: No


title: THA, Virus, Day 7, Rep 1


title: STL_293T_2

value: short, capped RNA


title: STL_293T_1


title: 9L_M_1127


title: CBX, Virus, Day 3, Rep 2


title: CBX, Virus, Day 3, Rep 4


title: THA, Virus, Day 6, Rep 4

value: Day 6


title: THA, Virus, Day 6, Rep 3


title: 9L_M_1126


title: STL_293T_unlab


title: 9L_M_1125


title: THA, Virus, Day 6, Rep 2


title: 9L_M_1122


title: TTTL_293T_1


title: THA, Virus, Day 5, Rep 4

value: Day 5


title: THA, Virus, Day 3, Rep 2

value: Brain


title: cytoplasm_ml240_ncrme6

city: London

first: Oliver

last: Ziff

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
 mRNA sequencing reads were processed using the nf-core/rna-seq v3.8.1 pipeline.  were assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Raw reads underwent adaptor trimming with Trim Galore, removal of ribosomal RNA with SortMeRNA, alignment to Ensembl GRCh38.99 human reference genome using splice-aware aligner, STAR v2.6.1 and BAM level quantification with Salmon to enable transcript level counting.
Detailed quality control of raw and aligned reads were assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Assembly: Ensembl GRCh38.99
Supplementary files format and content: Salmon quantified gene abundance per sample

growth_protocol: iPSCs were maintained with Essential 8 Medium media (Life Technologies) on Geltrex (Life Technologies) at 37°C and 5% carbon dioxide. iPSCs were passaged when reaching 70% confluency using EDTA (Life Technologies, 0.5 mM). PSC were plated to 100% confluency and then differentiated to a spinal neural precursor fate by a sequential treatment with small molecules, 0-7: 1μM Dorsomorphin (Millipore), 2μM SB431542 (Tocris Bioscience), and 3.3μM CHIR99021 (Miltenyi Biotec), day 7-14: 0.5μM retinoic acid (Sigma) and 1μM Purmorphamine (Sigma), day 14-18: 0.1μM Purmorphamine. After neural conversion and patterning, 0.1μM Compound E (Enzo Life Sciences) was added to promote terminal differentiation into spinal cord motor neurons.

extract_protocol:
iPSNs underwent subcellular fractionation into nuclear and cytoplasmic compartments using the Ambion PARIS kit cell fractionation buffer, following the manufacturer’s general protocol and an 8M urea nuclear lysis buffer (50mM Tris-HCL (pH8), 100mM NaCl, 0.1% SDS, and 1mM DTT).
Paired-end poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from nuclear and cytoplasmic fractions using the NEBNext® Ultra II Directional RNA Library kit for Illumina®, with 500ng of total RNA as input.

treatment_protocol: For VCP inhibitor treatment, at day 24 of motor neuron differentiation, medium was changed to fresh medium containing 1 μM of ML240 (Sigma; SML1071; CAS: 1346527-98-7), or the same percentage of DMSO for 2 h before harvesting.

value: ipsn

value: vcp knock-in

tag: strandedness

value: reverse

tag: fraction

value: cytoplasm


title: cytoplasm_ml240_tdpn1

value: tardbp mutant

tag: treatment


title: THA, Virus, Day 5, Rep 2

value: Infected with VEEV-TC


title: 9L_M_1124


title: THA, Virus, Day 5, Rep 1

value: thalamus


title: 9L_M_1123


title: THA, Virus, Day 1, Rep 4

value: Day 1


title: THA, Virus, Day 3, Rep 1

value: Day 3


title: 9L_M_1121


title: cytoplasm_ml240_tdpn2

tag: cell line


title: THA, Virus, Day 1, Rep 3


title: 9L_M_1120


title: cytoplasm_ml240_cb1d

value: vcp mutant


title: cytoplasm_ml240_ncrmc2


title: cytoplasm_ml240_glib

source_name: glib

value: glib


title: cytoplasm_ml240_cb1e


title: THA, Virus, Day 5, Rep 3


title: THA, Virus, Day 6, Rep 1


title: THA, Virus, Day 3, Rep 4


title: TC28a2 cells, Mocetinostat treated, replicate 3

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

data_processing:
The high throughput RNAseq data were analyzed using nf-core/RNA-seq pipeline v1.4.2 (https://github.com/nf-core/rnaseq).
Briefly, the reads were trimmed for adapters, and ribosomal RNA reads were removed. The remaining reads were aligned to the human reference genome using STAR v2.6.1d, and raw gene counts were obtained using featureCounts v1.6.4. This was followed by differential gene expression analysis using the Bioconductor DESeq2 R package v1.20.0.
Assembly: Ensembl GRCh38 release 98
Supplementary files format and content: tsv file with raw gene counts

extract_protocol:
Total RNA was isolated with Direct-zol RNA MicroPrep kit (Zymo Research) according to manufacturer’s protocol.
Libraries were constructed using an early access High Throughput RNAseq Prep kit (Jumpcode Genomics).

value: Immortalized human chondrocytes

value: Mocetinostat


title: TC28a2 cells, Mocetinostat treated, replicate 2


title: THA, Virus, Day 1, Rep 2


title: 9L_M_112


title: THA, Virus, Day 3, Rep 3


title: TC28a2 cells, Mocetinostat treated, replicate 1


title: cytoplasm_ml240_glia

source_name: glia

value: glia


title: cytoplasm_ml240_ctrl6

value: wildtype


title: 9L_M_1119


title: STX, Virus, Day 7, Rep 4

value: sensory cortex

value: Day 7


title: cytoplasm_ml240_ctrl4

value: ipsn


title: STX, Virus, Day 7, Rep 3

value: Brain


title: TC28a2 cells, DMSO treated, replicate 3

value: DMSO


title: TC28a2 cells, DMSO treated, replicate 2


title: 9L_M_1117


title: cytoplasm_ml240_ctrl3

value: reverse

value: cytoplasm


title: STX, Virus, Day 7, Rep 2

value: Infected with VEEV-TC


title: STX, Virus, Day 7, Rep 1


title: TC28a2 cells, DMSO treated, replicate 1


title: 9L_M_1115


title: nucleus_ml240_tdpn2

value: tardbp mutant

value: nucleus


title: 9L_M_1116


title: cytoplasm_ml240_ctrl1


title: THA, Virus, Day 1, Rep 1

value: thalamus

value: Day 1


title: STX, Virus, Day 6, Rep 4

value: Day 6


title: nucleus_ml240_tdpn1


title: 9L_M_1114


title: nucleus_ml240_ncrmc2

value: vcp knock-in


title: TRC105M1043_1

data_processing:
RNA-seq processing:
Single-end 76-bp sequenced reads were analyzed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v.0.10.1. Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 using Bowtie v.1.0.0 and SAMtools v.0.1.1.9, allowing two mismatches and 20 multihits. Differential expression was calculated with Cufflinks v.2.2.1 using the human GRCh37/hg19 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml. GSEAPreranked was used to perform GSEA of the described gene signatures on a pre-ranked gene list, setting 1,000 gene set permutations.
Assembly: GRCh37
Supplementary files format and content: Normalized counts obtained with Cuffnorm (Cufflinks)

source_name: STS26T xenografts treated with anti-ENG mAbs (TRC105/M1043)

growth_protocol: STS26T cells were maintained in high glucose Dulbecco's modified Eagles's medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 1mM sodium piruvate and 20 µg/ml gentamicin at 37ºC in a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen). After the recovery of the aqueous phase using chlorophorm, a DNAse treatment was performed using the Mini RNeasy kit (Qiagen) following manufacturer instructions.  cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit, and sequenced on a Illumina HiSeq2500 sequencer.
Total RNA samples (1µg) were used. Average sample RNA Integrity Number was 9.8 (range 9.6-10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) as recommended by the manufacturer. This kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 500 by following manufacturer's protocols.

treatment_protocol: Mice bearing STS26T xenografts were treated with TRC105 and M1043 anti-ENG mAbs (TRACON Pharmaceuticals; 10 mg/Kg twice a week, intraperitoneally) or the corresponding IgG control (10 mg/Kg twice a week, intraperitoneally).

value: Tissue:MPNST tumor. Cell line:STS26T human MPNST cell line (ATCC)

value: TRC105/M1043 anti-ENG mAbs


title: STX, Virus, Day 6, Rep 2


title: TRC105M1043_2


title: 9L_M_1113

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: STX, Virus, Day 6, Rep 3


title: 9L_M_1118


title: STX, Virus, Day 6, Rep 1


title: nucleus_ml240_cb1e

value: vcp mutant


title: IgG-control_3

source_name: STS26T xenografts treated with IgG control

value: IgG isotype control


title: 9L_M_1112


title: 9L_M_1111


title: IgG-control_2


title: nucleus_ml240_cb1d


title: STX, Virus, Day 5, Rep 4

value: sensory cortex

value: Day 5


title: 9L_M_1110


title: STX, Virus, Day 5, Rep 3

value: Brain


title: IgG-control_1


title: TRC105M1043_3


title: ChIP_S2_Input_1 fly

description:
ChIP Input DNA
Input DNA was aligned to fly genome and used as reference for generation of FE bigWig files.

organism: Drosophila melanogaster

source_name: S2 cells

extract_protocol:
S2 cells were washed twice with PBS and crosslinked with 1% formaldehyde (Pierce) for 10 min at room temperature. Crosslinking was quenched with 125 mM (final) glycine for 5 min and washed twice with PBS. Cells were lysed in 4 ml lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), 1x Protease inhibitor (Roche) for 10 min on ice. Lysed cells were centrifuged at 4,000 rpm for 5 min at 4°C and washed twice with 4 ml cold wash buffer (10 mM Tris-Cl pH 7.5, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0), 1x protease inhibitors. The pellet was resuspended in 1 ml shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris pH 7.5), 1x protease inhibitor and sheared on Covaris S220 (140 W, 5% duty factor, 200 bursts per cycle, 4°C) for 12 min (determined by time course optimization experiment). Extract was diluted with Triton X-100 (1% final) and NaCl (150 mM final) and cleared by centrifugation at 21,000g, 4°C for 10 min. For input, 10% of material was set aside. Cleared extract was supplemented with 4 μL of antibody and 75 nM competitor peptide and incubated overnight at 4°C. Immuno-precipitated chromatin was captured on 30 μl of Dynabeads protein G (Invitrogen) at 4°C for 1.5 hours. Beads were washed twice with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 150 mM NaCl), twice with high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM HEPES–potassium hydroxide pH 7.5, 500 mM NaCl), once with LiCl Buffer (100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% sodium deoxycholate) and once with TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Enriched DNA was eluted in 100 μl of proteinase K buffer (20mM HEPES pH 7.5, 1 mM EDTA, 0.5% SDS) supplemented with 40 μg of proteinase K (Ambion) for 30 min at 50°C. Formaldehyde crosslinks were reversed by adding NaCl (150 mM final) and 0.25 μg DNase-free RNase (Roche), followed by incubation overnight at 65°C. DNA was isolated using QIAquick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared based on a protocol adapted from Bowman et al., BMC Genomics 2013. DNA ends were first polished in a reaction containing NEB T4 Ligase Buffer, NEB T4 PNK, NEB T4 DNA Polymerase, and NEB Klenow DNA Polymerase. After minElute PCR purification (Quiagen), A-tailing was performed using NEB buffer #2 and NEB Klenow 3'-5' exo minus. Adapter ligations were performed using the NEB Blunt/TA Ligase Mastermix and 1 uM mPE Universal Adapters (A.U1 + A.U2). Libraries were amplified and indexed by PCR amplification using 2x Phusion Mastermix, PCR.U universal primer, and PCR.X indexing primers (6-10 cycles).  Indexed libraries were then cleaned by 1.5x SPRI bead purification.

treatment_protocol: For ChIP-seq, S2 cells were heat shocked at 37C for 1 hour.

value: WT S2

tag: s4u feed

value: No


title: nucleus_ml240_glia

value: ipsn

value: glia

value: reverse


title: 9L_M_111


title: STX, Virus, Day 5, Rep 2

value: Infected with VEEV-TC


title: 9L_M_1109


title: nucleus_ml240_ctrl6

value: wildtype

value: nucleus


title: ChIP_S2_panKacme_H4Kacmecomp_2


title: 9L_M_1108


title: STX, Virus, Day 5, Rep 1


title: STX, Virus, Day 3, Rep 4

value: Day 3


title: ChIP_S2_panKacme_H4Kacmecomp_1


title: ChIP_S2_panKacme_H4Kaccomp_2


title: 9L_M_1107


title: 9L_M_1106


title: STX, Virus, Day 3, Rep 3


title: ChIP_S2_panKacme_H4Kaccomp_1


title: STX, Virus, Day 3, Rep 2


title: nucleus_ml240_ctrl3


title: ChIP_S2_panKacme_nocomp_2


title: 9L_M_1104


title: STX, Virus, Day 3, Rep 1


title: cytoplasm_untreated_tdpn2

value: tardbp mutant

value: untreated

value: cytoplasm


title: nucleus_ml240_ctrl1


title: ChIP_S2_panKacme_nocomp_1


title: STX, Virus, Day 1, Rep 4

value: Day 1


title: nucleus_ml240_glib

value: glib

value: vcp mutant


title: 9L_M_1105


title: cytoplasm_untreated_tdpn1


title: 9L_M_1103


title: 9L_M_1102


title: STX, Virus, Day 1, Rep 3

value: sensory cortex


title: cytoplasm_untreated_ncrme6

value: vcp knock-in


title: cytoplasm_untreated_ncrmc2


title: nucleus_ml240_ctrl4


title: 9L_M_1101


title: H4Kac_S2_HS_2

description: H4Kac HS rep 2

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to dm6 or hg38 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Assembly: dm6, hg38
Supplementary files format and content: bigwig files of fold enrichment tracks over input control
Supplementary files format and content: narrowPeak peak files from MACS2

source_name: Fruit fly derived cells

extract_protocol:
20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols.

value: S2 cells

tag: antibody

value: Heat shock

tag: experiment

value: ChIP-seq


title: H4Kac_S2_HS_1

description: H4Kac HS rep 1


title: Kacme_S2_HS_2

description: Kacme HS rep 2

value: In house Kacme


title: STX, Virus, Day 1, Rep 1

value: Brain


title: 9L_M_1100


title: HIP, Virus, Day 7, Rep 4

value: hippocampus

value: Day 7

value: Infected with VEEV-TC


title: cytoplasm_untreated_cb1e

value: ipsn

value: reverse


title: cytoplasm_untreated_glib

value: untreated


title: HIP, Virus, Day 7, Rep 3


title: cytoplasm_untreated_cb1d

value: cytoplasm


title: H4Kac_S2_2

description: H4Kac rep 2


title: H4Kac_S2_1

description: H4Kac rep 1


title: 9L_M_11


title: HIP, Virus, Day 7, Rep 2


title: cytoplasm_untreated_glia

value: glia


title: Kacme_S2_HS_1

description: Kacme HS rep 1


title: 9L_M_110


title: cytoplasm_untreated_ctrl6

value: wildtype


title: HIP, Virus, Day 7, Rep 1


title: Kacme_S2_2

description: Kacme rep 2


title: 9L_M_1099


title: Kacme_S2_1

description: Kacme rep 1


title: cytoplasm_untreated_ctrl4


title: 9L_M_1097


title: HIP, Virus, Day 6, Rep 4

value: Day 6


title: LP

city: Saint Louis

first: Jonathan

last: Kipnis

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description:
RNA was isolated from the brains of 18 flies.
KLAA-LP-LP_S3_L002

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: dm6
Supplementary_files_format_and_content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: brain

growth_protocol: Not applicable

extract_protocol:
10x Genomics Chromium single-cell preparation
NGS Illumina Next Seq

treatment_protocol: conventionally reared flies (CTRL), antibiotic-treated (8 days) flies (ABX) and Lactiplantibacillus plantarum-transferred (5-day ABX treatment + 3-day LP transfer) flies (LP)

value: Lactiplantibacillus plantarum-transferred (5-day ABX treatment + 3-day LP transfer) (LP)

value: 8 days

tag: Sex

value: male

value: brain


title: STX, Virus, Day 1, Rep 2

value: sensory cortex

value: Day 1

tag: genotype


title: cytoplasm_untreated_ctrl3


title: HIP, Virus, Day 6, Rep 3

value: Brain


title: HIP, Virus, Day 6, Rep 2

value: hippocampus


title: ABX

description:
RNA was isolated from the brains of 18 flies.
KLAA-ABX-ABX_S1_L001

value: antibiotic-treated (8 days) (ABX)


title: 9L_M_1095

source_name: C57BL/6J Male P56 Mouse Brain


title: cytoplasm_untreated_ctrl1


title: 9L_M_1096


title: CTRL

description:
RNA was isolated from the brains of 18 flies.
KLAA-Ctrl-Ctrl_S2_L002

value: conventionally reared (CTRL)


title: HIP, Virus, Day 6, Rep 1

value: Infected with VEEV-TC


title: 9L_M_1098


title: nucleus_untreated_tdpn2

value: ipsn

value: tardbp mutant

value: reverse

value: nucleus


title: 9L_M_1094


title: HIP, Virus, Day 5, Rep 3

value: Day 5


title: nucleus_untreated_ncrme6

value: vcp knock-in

value: untreated


title: Input_S2

description: Input

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to dm6 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files of fold enrichment tracks over input control
Supplementary_files_format_and_content: narrowPeak peak files from MACS2

growth_protocol: S2 cells were cultured in Schneider's Drosophila medium with 10% heat-inactivated fetal bovine serum (FBS), and 1% Penicillin/Streptomycin.

extract_protocol:
30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols.

treatment_protocol: For heat shock samples, cells were incubated at 37 degrees C for one hour

value: S2 cells

value: Input


title: 9L_M_1093


title: 9L_M_1092


title: nucleus_untreated_tdpn1


title: 9L_M_1091


title: HIP, Virus, Day 5, Rep 2


title: nucleus_untreated_ncrmc2


title: 7 dpa, scRNA-seq

city: Eugene

first: Victor

last: Lewis

state: Oregon

address: 1255 Mill St

department: Institute of Molecular Biology

institute: University of Oregon

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Pseudoalignment and processing of raw reads was done in Kallisto/Bustools (https://github.com/pachterlab/kb_python) to generate a cell data set for Monocle3 (https://cole-trapnell-lab.github.io/monocle3/)
Assembly: GRCz11.99
Supplementary files format and content: rds file of cell_data_set

organism: Danio rerio

source_name: Caudal fin

extract_protocol:
Tissue from 20 adult zebrafish was pooled for each group. Regenerative caudal fin tissue was collected into 1x PBS on ice, diced, then washed with L-15 media supplemented with 1X GlutaMax, 1X Antibiotic-Antimycotic and 1X Penicillin-Streptomycin (all Thermo Fisher). The tissue was then enzymatically digested using 0.25% Trypsin-EDTA (Thermo Fisher) and Liberase DL (2 mg/ml, Sigma) at room temperature for 20 min followed by mechanical dissociation by pipet titration every 5 minutes. Enzymatic digestion was inhibited by the addition of 20% fetal bovine serum. Cells were filtered through a 100 μm cell strainer and then pelleted by centrifugation at 0.2 g for 2.5 minutes. The cell pellet was washed with PBS and re-suspended in PBS + 0.04% bovine serum albumin.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells from fin tissue were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up, amplified by PCR, and the appropiate sized fragments were selected for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Caudal fin

tag: time

value: 7 dpa

tag: Stage

value: Adult


title: 3 dpa, scRNA-seq

description: 10x Genomics

value: 3 dpa


title: HIP, Virus, Day 5, Rep 1

value: Brain

value: hippocampus

tag: timepoint(dpi)


title: nucleus_untreated_cb1e

value: vcp mutant


title: 9L_M_1090

tag: brain region


title: siGPR137_3_EXPA

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

data_processing:
Basecalling RTA 2.4.11, Illumina instrument run time analysis software
Demultiplexing, Bcl2fastq v2.17
Filtering (Adaptor and quality), Cutadapt 1.18
Alignment, STAR 2.7.0f
Counts were calculated in PartekFlow v8 and processed with R version 4.0.3  using the edgeR 3.31.4 R package. Batch effects from different sequencing experiments were removed using the removeBatchEffect R function from the limma 3.45.14 R package using siCon samples as reference. Differential expression analysis against siCon cells was performed using the limma 3.45.14 R package.
Assembly: hg19
Supplementary files format and content: "Gene_counts-no batch corrected.txt" contains the raw gene counts without normalization or batch correction for different experiments
Supplementary files format and content: "logcpm_TMM_normalized_GPCR_BatchCorrected.txt" contains normalized and batch corrected counts

source_name: skin

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2 and cultured in EPILIFE medium (Life Technologies) with Human Keratinocyte Growth Supplement (HKGS, Life Technologies).

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transfected with the corresponding siRNAs one day after plating and were harvested 72hs after transfection. siRNAs were from Dharmacon/ Horizon Discovery; ON-TARGET plus SMARTpool: LTB4R (L-005653-00), HCAR3 (L-005628-02), GPR153 (L-027388-00), GPR137 (L-005439-01), and non-targeting control siRNA (D-001810-10). siRNA was transfected at a concentration of 15 pmol/well for 6-well plates using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions.

value: Primary neonatal pooled human keratinocytes

value: skin

tag: batch

value: EXPA

tag: replicate


title: nucleus_untreated_cb1d

value: ipsn

value: reverse


title: siGPR137_2_EXPA

tag: tissue


title: HIP, Virus, Day 3, Rep 4

value: Day 3

value: Infected with VEEV-TC


title: HIP, Virus, Day 3, Rep 3


title: nucleus_untreated_glib

tag: cell type

value: glib

value: untreated

value: nucleus


title: siGPR137_1_EXPA


title: 9L_M_1089

tag: age

tag: strain


title: siCon_3_EXPA

tag: treatment

value: siCon


title: HIP, Virus, Day 5, Rep 4

value: Day 5


title: 9L_M_1088


title: nucleus_untreated_ctrl6

tag: cell line

value: wildtype

tag: strandedness

tag: fraction


title: 9L_M_1087


title: HIP, Virus, Day 3, Rep 1


title: HIP, Virus, Day 1, Rep 4

value: Day 1


title: siCon_1_EXPA


title: siCon_2_EXPA


title: HIP, Virus, Day 1, Rep 3

value: Brain


title: nucleus_untreated_ctrl3


title: 9L_M_109


title: HIP, Virus, Day 1, Rep 2

value: hippocampus


title: 9L_M_1085


title: H1, D95

city: Helsinki

first: Juho

middle: Eemil

last: Pitkonen

address: Haartmaninkatu 8

department: Physiology

country: Finland

institute: University of Helsinki

description:
pvalue_ordered_results_dds_D95-vs-D0_H1-DESeq.txt
pvalue_ordered_results_dds_D95_1_solulinjaDESeq.txt

data_processing:
Total of 20–30 millions reads per sample were sequenced and aligned using STAR v2.7.0 that uniquely mapped 80%–90% of the reads on the GRCh38 human genome, after quality trimming of 25 nucleotides from the 3′-ends of the transcripts (discarding reads shorter than 30 nucleotides) using cutadapt v1.8.1.
Differential expression analysis was performed with the R package DESeq2 using a design formula that models the cell line difference at time 0, the difference over time, and any genotype-specific difference over time (by using the interaction term genotype: time).
The likelihood ratio test removed any genotype-specific differences over time. Principal component analysis (PCA) showed six outliers (one replicate of undifferentiated cells, two at D30, and one at D95 of controls, and one iPSC FXS sample), which were removed from the analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of H1 and FMR1 KO samples with mean reads, and log2fold changes compared to D0 stage of each cell line for standardization. P-values and P-adjusted values included.
Supplementary files format and content: Tab-delimited text files of FMR1-KO lines with mean reads and log2fold changes compared to isogenic CTRL cell line at the same differentation stage for standardization. P-values and P-adjusted values included.

source_name: Astroglia

growth_protocol: Human pluripotent stem cells (hPSCs) were maintained on Matrigel-coated plates in Essential 8 medium. Astrocytes were differentiated as previously described (Peteri et al., 2020). Briefly, for differentiation, 80% confluent hPSCs were dissociated with 0.5 mM ethylenediaminetetraacetic acid and plated on low-attachment 6-well plate in E8 with 20 ng/ml human basic fibroblast growth factor and 20 μM Rho kinase inhibitor. On the following day, medium was changed to neuronal induction medium (Advanced DMEM/F12, 1X N2, 2 mM L-glutamine, 1X nonessential amino acids [NEAA], and 1X penicillin–streptomycin [P–S] supplemented with 0.1 μM LDN-193189, 1 μM cyclopamine 10 μM SB-431542, and 0.5 μg/ml DKK1 for culturing the first 12 days. Thereafter, neural progenitors were cultured in neuronal induction medium supplemented with 20 ng/ml brain-derived neurotrophic factor until day 30 (D30) and in neurosphere medium (Advanced DMEM/F12, 1X B27 -RA, 1X L-glutamate, 1X NEAA, 1X P–S ) supplemented with 20 ng/ml bFGF2 and 20 ng/ml epidermal growth factor until D60. Growth factors were added three times a week and spheres were dissociated approximately once per week manually. At D60, spheres were dissociated and progenitors plated on poly-ornithine/laminin-coated  culture plates in neurosphere medium supplemented with 20 ng/ml ciliary neurotrophic factor. Cells were passaged with Trypsin–EDTA (0.05%) approximately once per week and seeded at 20,000 cells/cm2. After D75, cells had acquired astrocyte morphology and they were maintained on Matrigel-coated culture plates.

extract_protocol:
Total cellular RNA was extracted using NucleoSpin RNA kit (QIAGEN) according to the manufacturer's instructions.
Library construction was made with Nugen Ovation Universal RNAseq Kit according to package instructions using isolated RNA.

value: Astroglia

value: control

value: D90 Astrosytes


title: Input_K562

description: Input

source_name: Human leukemia derived cell line

value: K562 cells

tag: antibody

value: Input

tag: experiment


title: HIP, Virus, Day 1, Rep 1

tag: genotype


title: 9L_M_1083


title: 9L_M_1084


title: H1FMR1-KO, D95

description:
pvalue_ordered_results_dds_D95-vs-D0_H1_Fmr1_KO-DESeq.txt
pvalue_ordered_results_dds_D95_1_solulinjaDESeq.txt

value: FMR1 KO


title: H1FMR1-KO, D60

description:
pvalue_ordered_results_dds_D60-vs-D0_H1_Fmr1_KO-DESeq.txt
pvalue_ordered_results_dds_D60_solulinjaDESeq.txt

source_name: Neural progenitors

value: Neural progenitors

value: D60 Neuroprogenitors


title: MTX, Virus, Day 7, Rep 4

value: motor cortex

value: Day 7

value: Infected with VEEV-TC


title: H1, D60

description:
pvalue_ordered_results_dds_D60-vs-D0_H1-DESeq.txt
pvalue_ordered_results_dds_D60_solulinjaDESeq.txt


title: HIP, Virus, Day 3, Rep 2

value: Day 3


title: Input_293T

description: Input

source_name: Human embryonic kidney derived cells

value: HEK293T cells


title: H4Kac_cutrun_2

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to dm6 or hg38 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Assembly: dm6, hg38
Supplementary files format and content: bigwig files of fold enrichment tracks over input control
Supplementary files format and content: narrowPeak peak files from MACS2
Library strategy: CUT&RUN

value: CUT&RUN


title: H1FMR1-KO, D30

description:
pvalue_ordered_results_dds_D30-vs-D0_H1_Fmr1_KO-DESeq.txt
pvalue_ordered_results_dds_D30_solulinjaDESeq.txt

value: D30 Neuroprogenitors


title: 9L_M_1086


title: H4Kac_cutrun_1


title: MTX, Virus, Day 7, Rep 2

value: Brain


title: H1, D30

description:
pvalue_ordered_results_dds_D30-vs-D0_H1-DESeq.txt
pvalue_ordered_results_dds_D30_solulinjaDESeq.txt


title: 9L_M_108


title: MTX, Virus, Day 7, Rep 1


title: Kacme_cutrun_2

value: In house Kacme


title: H1FMR1-KO, D0

description: pvalue_ordered_results_dds_D0_solulinjaDESeq.txt

value: D0 Neuroprogenitors


title: H1, D12

description:
pvalue_ordered_results_dds_D12-vs-D0_H1-DESeq.txt
pvalue_ordered_results_dds_D12_solulinjaDESeq.txt

value: control

value: D12 Neuroprogenitors


title: 9L_M_1075


title: 9L_M_1082


title: MTX, Virus, Day 6, Rep 2

value: Day 6


title: Kacme_cutrun_1

value: K562 cells


title: 9L_M_1074


title: MTX, Virus, Day 6, Rep 3


title: 9L_M_1077


title: H4Kac_K562_2

value: ChIP-seq


title: SUPT5H_Day8_3

description:
RNAseq library
D8_SPT5_3893_S15

data_processing:
Alignement with STAR (custom scripts available at https://github.com/churchmanlab)
Read counts of protein coding genes using featureCounts
nSolver Analysis Software used for extracting and normalizing Nanostring direct mRNA levels (RCC files)
Assembly: GRCh38
Supplementary files format and content: *.csv files contain read counts obtained from featureCounts on bam files

source_name: Bone Marrow

extract_protocol:
Qiazol extraction
RNA sequencing library preparation (SMART-Seq v4 )

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 8

value: SUPT5H gRNA


title: H4Kac_K562_1


title: H1, D0

value: Neural progenitors


title: 9L_M_1079


title: MTX, Virus, Day 6, Rep 1

source_name: Brain

value: motor cortex

tag: timepoint(dpi)

value: Infected with VEEV-TC


title: 9L_M_1072

tag: brain region


title: 9L_M_1073


title: H4Kac_293T_2

value: HEK293T cells


title: H1FMR1-KO, D12

description:
pvalue_ordered_results_dds_D12-vs-D0_H1_Fmr1_KO-DESeq.txt
pvalue_ordered_results_dds_D12_solulinjaDESeq.txt

value: FMR1 KO


title: SUPT5H_Day8_2

description:
RNAseq library
D8_SPT5_3881_S7


title: 9L_M_1081


title: AAVS1_Day8_3

description:
RNAseq library
D8_AAVS1_3893_S11

value: AAVS1 gRNA


title: 9L_M_1071


title: H4Kac_293T_1


title: 9L_M_1070


title: AAVS1_Day8_2

description:
RNAseq library
D8_AAVS1_3881_S3


title: Kacme_293T_2

value: In house Kacme


title: MTX, Virus, Day 5, Rep 2

value: Brain

value: Day 5


title: MTX, Virus, Day 3, Rep 4

value: Day 3


title: MTX, Virus, Day 5, Rep 4


title: Kacme_293T_1


title: Kacme_K562_1


title: 9L_M_1069


title: SUPT5H_Day8_1

description:
RNAseq library
D8_SPT5_3875_S15


title: 9L_M_107


title: MTX, Virus, Day 3, Rep 3