title: RMB1472


title: RMB1470

status: Public on Aug 08 2022

type: SRA

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

library_source: transcriptomic

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 downloaded from GENCODE using RSEM program version 1.2.19 with default parameters.
Gene expression values in transcripts per million (TPM) were calculated using the RSEM program and the mouse GENCODE gene annotation version M4.
Quality control and outlier cell detection was performed using Seurat R package.
Assembly: GRCm38
Supplementary files format and content: tab delimited TPM table

molecule: total RNA

organism: Mus musculus

extract_protocol:
single cells were captured on Fluidigm C1 mRNA Seq IFC and lysed and reverse-transcribed in situ
Nextera XT

tag: age


title: RMB1469


title: RMB1468


title: RMB1465


title: RMB544


title: RMB1466


title: RMB1464


title: RMB1467


title: RMB1463


title: RMB1461


title: RMB1462


title: RMB1460


title: RMB1458


title: RMB1459


title: RMB1457


title: RMB1456


title: RMB1455


title: RMB1454


title: RMB1481


title: RMB1452


title: RMB1451


title: RMB1448


title: RMB1449


title: RMB1450


title: RMB1446


title: RMB1444


title: RMB1445


title: RMB1442


title: RMB1443


title: RMB1440


title: RMB1441


title: RMB1439


title: RMB1438


title: RMB1437


title: RMB1435


title: RMB1436


title: RMB1434


title: RMB1431


title: RMB1432


title: RMB1453


title: RMB1429


title: RMB1430


title: RMB1427


title: RMB1447


title: RMB1424


title: RMB1425


title: RMB1423


title: RMB1422


title: RMB1421


title: RMB1420


title: RMB1426


title: RMB1417


title: RMB1419


title: RMB1418


title: RMB1416


title: RMB1415


title: RMB1412


title: RMB1414


title: RMB1411


title: RMB1433


title: RMB1410


title: RMB1409


title: RMB1428


title: RMB1408


title: RMB1407


title: RMB1404


title: RMB1403


title: RMB1406


title: RMB1402


title: RMB1405


title: RMB1397


title: RMB1400


title: RMB1401


title: RMB1399


title: RMB1398


title: RMB1395


title: RMB1413


title: RMB564


title: RMB1253


title: RMB1254


title: RMB1393


title: RMB1249


title: RMB1251


title: RMB1250


title: RMB1392


title: RMB1394


title: RMB1252


title: RMB1255


title: RMB1248


title: RMB1247


title: RMB1242


title: RMB1244


title: RMB1245


title: RMB1246


title: RMB1241


title: RMB1243


title: RMB1240


title: RMB1396


title: RMB1239


title: RMB1237


title: RMB1236


title: RMB1238


title: RMB1235


title: RMB1233


title: RMB1230


title: RMB1232


title: RMB1234


title: RMB1231


title: RMB1221


title: RMB1225


title: RMB1228


title: RMB1229


title: RMB1226


title: RMB1222


title: RMB1227


title: RMB1216


title: RMB1214


title: RMB1213


title: RMB1212


title: RMB1220


title: RMB1215


title: RMB1219


title: RMB1217


title: RMB1210


title: RMB1208


title: RMB1209


title: RMB1224


title: RMB1223


title: RMB1206


title: RMB1207


title: RMB1203


title: RMB1204


title: RMB1218


title: RMB1201


title: RMB1205


title: RMB1195


title: RMB1199


title: RMB1197


title: RMB1202


title: RMB1211


title: RMB1198


title: RMB1188


title: RMB1191


title: RMB1192


title: RMB1190


title: RMB1187


title: RMB1189


title: RMB1186


title: RMB1185


title: RMB1184


title: RMB1183


title: RMB1182


title: RMB1200


title: RMB1196


title: RMB1193


title: RMB1178


title: RMB1180


title: RMB1179


title: RMB1176


title: RMB1171


title: RMB1170


title: RMB1172


title: RMB1194


title: RMB1169


title: RMB1181


title: RMB1173


title: RMB1174


title: RMB1164


title: RMB1166


title: RMB1167


title: RMB1168


title: RMB1177


title: RMB1165


title: RMB1162


title: RMB1163


title: RMB1160


title: RMB1159


title: RMB1157


title: RMB1156


title: RMB1158


title: RMB1153


title: RMB1155


title: RMB1148


title: RMB1152


title: RMB1151


title: RMB1154


title: RMB1150


title: RMB1149


title: RHP6369


title: RMB1175


title: RHP6366


title: RMB1146


title: RHP6365


title: RHP6363


title: RHP6362


title: RHP6361


title: RHP6364


title: RHP6360


title: RMB1161


title: RMB1147


title: RHP6367


title: RHP6359


title: RHP6358


title: RHP6357


title: RHP6356


title: RHP6355


title: RHP6354


title: RHP6368


title: RHP6352


title: RHP6353


title: RHP6349


title: RHP6350


title: RHP6351


title: RHP6348


title: RHP6346


title: RHP6345


title: RHP6344


title: RHP6347


title: RHP6339


title: RHP6336


title: RHP6338


title: RHP6340


title: RHP6335


title: RHP6332


title: RHP6331


title: RHP6333


title: RHP6330


title: RHP6337


title: RHP6334


title: RHP6329


title: RHP6328


title: RHP6327


title: RHP6326


title: RHP6324


title: RHP6322


title: RHP6325


title: RHP6321


title: RHP6320


title: RHP6343


title: RHP6319


title: RHP6342


title: RHP6317


title: RHP6318


title: RHP6341


title: RHP6315


title: RHP6313


title: RHP6311


title: RHP6312


title: RHP6310


title: RHP6305


title: RHP6306


title: RHP6307


title: RHP6303


title: RHP6304


title: RHP6302


title: RHP6323


title: RHP6298


title: RHP6300


title: RHP6301


title: RHP6297


title: RHP6299


title: RHP6296


title: RHP6294


title: RHP6295


title: RHP6314


title: RHP6292


title: RHP6291


title: RHP6290


title: RHP6316


title: RHP6293


title: RHP6289


title: RHP6309


title: RHP6287


title: RHP6308


title: RHP6288


title: RMB857

value: Adult


title: RMB859


title: RMB849


title: RMB836


title: RMB843


title: RMB839


title: RMB832


title: RMB827


title: RMB825


title: RMB826


title: RMB820


title: RMB821


title: RMB808


title: RMB803


title: RMB795


title: RMB796


title: RMB798


title: RMB805


title: RMB792


title: RMB786


title: RMB793


title: RMB783


title: RMB779


title: RMB411


title: RMB780


title: RMB771


title: RMB3316


title: RMB3315


title: RMB3314


title: RMB824


title: RMB813


title: RMB3312


title: RMB810


title: RMB3313


title: RMB3310


title: RMB3311


title: RMB3309


title: RMB3307


title: RMB3308


title: RMB3306


title: RMB3305


title: RMB3304


title: RMB3302


title: RMB3300


title: RMB3303


title: RMB3299


title: RMB3298


title: RMB3297


title: RMB3296


title: RMB3293


title: RMB3292


title: RMB3295


title: RMB3290


title: RMB3286


title: RMB3287


title: RMB3284


title: RMB3288


title: RMB3289


title: RMB3285


title: RMB3282


title: RMB3281


title: RMB3283


title: RMB3276


title: RMB3301


title: RMB3274


title: RMB3279


title: RMB3272


title: RMB3278


title: RMB3270


title: RMB3294


title: RMB3277


title: RMB3273


title: RMB3266


title: RMB3291


title: RMB3265


title: RMB3268


title: RMB3275


title: RMB3280


title: RMB3262


title: RMB3271


title: RMB3264


title: RMB3269


title: RMB3261


title: RMB3263


title: RMB3258


title: RMB3257


title: RMB3259


title: RMB3260


title: RMB3256


title: RMB3253


title: RMB3255


title: RMB3254


title: RMB3252


title: RMB3251


title: RMB3267


title: RMB3249


title: RMB3248


title: RMB3250


title: RMB3247


title: RMB3246


title: RMB3245


title: RMB3244


title: RMB3243


title: RMB3242


title: RMB3236


title: RMB3240


title: RMB3238


title: RMB3237


title: RMB3235


title: RMB3234


title: RMB3231


title: RMB3232


title: RMB3233


title: RMB3229


title: RMB3228


title: RMB3226


title: RMB3225


title: RMB3230


title: RMB3224


title: RMB3223


title: RMB3227


title: RMB3220


title: RMB3241


title: RMB3222


title: RMB3218


title: RMB3221


title: RMB3219


title: RMB3239


title: RMB3217


title: RMB3216


title: RMB3215


title: RMB3211


title: RMB3213


title: RMB3214


title: RMB3209


title: RMB3208


title: RMB3212


title: RMB3207


title: RMB3206


title: RMB3203


title: RMB3201


title: RMB3205


title: RMB3202


title: RMB3199


title: RMB3200


title: RMB3198


title: RMB3197


title: RMB3194


title: RMB3195


title: RMB3193


title: RMB3210


title: RMB3196


title: RMB3188


title: RMB3187


title: RMB3192


title: RMB3184


title: RMB3189


title: RMB3190


title: RMB3183


title: RMB3182


title: RMB3185


title: RMB3204


title: RMB3180


title: RMB3181


title: RMB3174


title: RMB3175


title: RMB3172


title: RMB3177


title: RMB3178


title: RMB3191


title: RMB3186


title: RMB3169


title: RMB3168


title: RMB3165


title: RMB3167


title: RMB3171


title: RMB3166


title: RMB3170


title: RMB3163


title: RMB3162


title: RMB3179


title: RMB3156


title: RMB3158


title: RMB3159


title: RMB3160


title: RMB3157


title: RMB3155


title: RMB3161


title: RMB3176


title: RMB3173


title: RMB3154


title: RMB3153


title: RMB3151


title: RMB3150


title: RMB3152


title: RMB3149


title: RMB3164


title: RMB3148


title: RMB3147


title: RMB3146


title: RMB3145


title: RMB3143


title: RMB3144


title: RMB3141


title: RMB3142


title: RMB3139


title: RMB3140


title: RMB3137


title: RMB3131


title: RMB3129


title: RMB3133


title: RMB3135


title: RMB3134


title: RMB3132


title: RMB3130


title: RMB3128


title: RMB3136


title: RMB3127


title: RMB3126


title: RMB3088


title: RMB3125


title: RMB3089


title: RMB3086


title: RMB3087


title: RMB3085


title: RMB3084


title: RMB3082


title: RMB3080


title: RMB3081


title: RMB3138


title: RMB3083


title: RMB3078


title: RMB3076


title: RMB3077


title: RMB3075


title: RMB3071


title: RMB3070


title: RMB3067


title: RMB3072


title: RMB3073


title: RMB3069


title: RMB3068


title: RMB3074


title: RMB3062


title: RMB3061


title: RMB3066


title: RMB3060


title: RMB3065


title: RMB3063


title: RMB3079


title: RMB3057


title: RMB3058


title: RMB3054


title: RMB3053


title: RMB3052


title: RMB3051


title: RMB3049


title: RMB3055


title: RMB3050


title: RMB3048


title: RMB3044


title: RMB3047


title: RMB3046


title: RMB3043


title: RMB3064


title: RMB3042


title: RMB3045


title: RMB3041


title: RMB3059


title: RMB3056


title: RMB3039


title: RMB3037


title: RMB3040


title: RMB3031


title: RMB3036


title: RMB3034


title: RMB3033


title: RMB3030


title: RMB3032


title: RMB3029


title: RMB3035


title: RMB3028


title: RMB3026


title: RMB3025


title: RMB3023


title: RMB3022


title: RMB3021


title: RMB3019


title: RMB3016


title: RMB3020


title: RMB3038


title: RMB3018


title: RMB3013


title: RMB3014


title: RMB3011


title: RMB3005


title: RMB3003


title: RMB3004


title: RMB3008


title: RMB3027


title: RMB3006


title: RMB3002


title: RMB3012


title: RMB3001


title: RMB3010


title: RMB3024


title: RMB3000


title: RMB3007


title: RMB3009


title: RMB3017


title: RMB2999


title: RMB2998


title: RMB2997


title: RMB2995


title: RMB3015


title: RMB2994


title: RMB2992


title: RMB2991


title: RMB2990


title: RMB2989


title: RMB2988


title: RMB2986


title: RMB2987


title: RMB2985


title: RMB2983


title: RMB2984


title: RMB2979


title: RMB2982


title: RMB2981


title: RMB2977


title: RMB2980


title: RMB2975


title: RMB2974


title: RMB2993


title: RMB2972


title: RMB2973


title: RMB2971


title: RMB2996


title: RMB2976


title: RMB2970


title: RMB2969


title: RMB2968


title: RMB2967


title: RMB2966


title: RMB2965


title: RMB2964


title: RMB2963


title: RMB2961


title: RMB2978


title: RMB2962


title: RMB2960


title: RMB2958


title: RMB2957


title: RMB2959


title: RMB2953


title: RMB2956


title: RMB2955


title: RMB2954


title: RMB2952


title: RMB2950


title: RMB2949


title: RMB2946


title: RMB2947


title: RMB2942


title: RMB2943


title: RMB2941


title: RMB2940


title: RMB2945


title: RMB2939


title: RMB2937


title: RMB2938


title: RMB2935


title: RMB2936


title: RMB2931


title: RMB2933


title: RMB2932


title: RMB2934


title: RMB2930


title: RMB2951


title: RMB2929


title: RMB2928


title: RMB2926


title: RMB2948


title: RMB2944


title: RMB2927


title: RMB2922


title: RMB2923


title: RMB2920


title: RMB2919


title: RMB2921


title: RMB2918


title: RMB2917


title: RMB2916


title: RMB2915


title: RMB2914


title: RMB2913


title: RMB2912


title: RMB2925


title: RMB2909


title: RMB2911


title: RMB2910


title: RMB2907


title: RMB2901


title: RMB2906


title: RMB2902


title: RMB2908


title: RMB2924


title: RMB2899


title: RMB2905


title: RMB2904


title: RMB2903


title: RMB2897


title: RMB2900


title: RMB2894


title: RMB2895


title: RMB2893


title: RMB2891


title: RMB2896


title: RMB2890


title: RMB2889


title: RMB2888


title: WT + T. gondii infection (rep2)

city: Bethesda

first: Neelam

last: Redekar

state: MD

address: 9000 rockville pike

department: NIAID

country: USA

institute: NIH

data_processing:
Illumina sequencing data was demultiplexed and mapped to mouse transcriptome reference (refdata-gex-mm10-2020-A) using Cellranger (v4.0.0).
Genome_build: mm10 (refdata-gex-mm10-2020-A)
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix (counts, barcodes, features)

source_name: CD11c+ splenocytes

extract_protocol:
CD11c+ splenocyte were isolated from single cell suspensions of splenocytes using CD11c MicroBeads (Militenyi Biotec, Cat# 130-125-835) according to the manufacturer’s instructions.
Chromium Single Cell 3’ Reagent Kits v3.1 (10X Genomics)

tag: strain

tag: genotype

value: Wildtype

tag: treatment

value: T. gondii infection

tag: groups

value: WT + T. gondii infection


title: Bcl3 flx/flx Zbtb46 cre KO mice + T. gondii infection (rep2)

value: Bcl3 flx/flx Zbtb46 cre KO mice


title: RMB2887


title: RMB2898


title: Bcl3 flx/flx Zbtb46 cre KO mice uninfected (rep2)

value: uninfected


title: WT uninfected (rep1)

value: WT uninfected


title: RMB2884


title: RMB2886


title: RMB2885


title: Bcl3 flx/flx Zbtb46 cre KO mice uninfected (rep1)


title: RMB2882


title: Bcl3 flx/flx Zbtb46 cre KO mice + T. gondii infection (rep1)


title: RMB2879


title: RMB2883


title: RMB2878


title: RMB2881


title: RMB2877


title: RMB2876


title: RMB2880


title: WT uninfected (rep2)


title: RMB2892


title: RMB2875


title: RMB2874


title: Astrocytes, MCAO + non-exercise

type: RNA

city: Kusatsu

first: Natsumi

last: Yamaguchi

state: Shiga

address: 1-1-1 Noji-Higashi

country: Japan

institute: Ritsumeikan University

description: Astrocytic transcriptome 15 days after focal cerebral ischemia

hyb_protocol: Fragmented and biotin-labeled ss-cDNA samples were mixed with Hybridization Master Mix and incubated for 5 minutes at 99℃ in tubes or 95℃ in plates, then for 5 minutes at 45℃ in a thermal cycler. The array was placed into hybridization oven trays {GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientific, Inc.)} and incubated with rotation at 60 rpm for 16 hours at 45℃. After hybridization, microarrays were washed using GeneChip™ Fluidics Station 450 (Thermo Fisher Scientific, Inc.).

scan_protocol: Scanning was performed on GeneChipTM Scanner 3000 7G System (Thermo Fisher Scientific, Inc.).

data_processing: The scanned images were analyzed with Expression Console™ Software (Thermo Fisher Scientific, Inc.). Normalization was performed by SST-RMA.

label: Biotin

source_name: Cortices, non-exercise, 15 days after cerebral ischemia

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin {GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.)}.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Thermo Fisher Scientific, Waltham, MA, USA) from the sorted astrocytes. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: Cortex

tag: cell type

value: sorted astrocytes

tag: gender

value: Male

value: 7 weeks

value: MCAO + non-exercise


title: RMB2873


title: Astrocytes, MCAO + exercise

source_name: Cortices, exercise, 15 days after cerebral ischemia

value: MCAO + exercise


title: RMB2872


title: RMB2871


title: WT + T. gondii infection (rep1)


title: RMB2870


title: RMB2869


title: RMB2868


title: RMB2867


title: RMB2864


title: CUT&RUN sequencing of scrambled control A375 cells (RNA pol II antibody) [RNAPII_shSCR]

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
library strategy:CUT&RUN
Raw reads were analyzed with FastQC for quality control, and STAR alignment (--alignIntronMax 1) was used to generate bam files.
Bedgraph file was generated with bedtools
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include DESeq2 normalized values for each Sample
Supplementary files format and content: Bedgraph file

molecule: genomic DNA

organism: Homo sapiens

source_name: Melanoma

extract_protocol:
After purification of the extracted DNA with DNA Purification Buffers and Spin Columns kit (Cell Signaling Technologies). Size selection was performed using SPRIselect beads (Beckman Coulter) and fragment sizes were determined with an Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent). The double stranded DNA content of the libraries were quantified with Qubit 3.0 using the Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific) followed by equimolar pooling of the indexed libraries.
Sequencing libraries were generated using NEBNext ULTRA II DNA library Prep Kit for Illumina (New England Biolabs) with indexed NEBNext Multiplex Oligos for Illumina (New England Biolabs)

value: Melanoma

tag: cell line

value: Scrambled control permeablized with digitonin, incubated with RNA Pol II antibody, followed by DNA digestion with pAG-MNase


title: CUT&RUN sequencing of A375 cells (IgG control antibody) [IgG]

value: permeablized with digitonin, incubated with IgG control antibody, followed by DNA digestion with pAG-MNase


title: CUT&RUN sequencing of TRIM28 knockdown A375 cells (RNA pol II antibody) [RNAPII_shT28]

value: TRIM28 knockdown permeablized with digitonin, incubated with RNA Pol II antibody, followed by DNA digestion with pAG-MNase


title: A375 cells transduced with pBABE-JUNB retrovirus [JUNB_2]

data_processing:
Basecalling and demultiplexing was performed using CASAVA software with default settings
Sequences were aligned to hg38 using STAR with default settings
Normalized gene expression matrix was generated with DESeq2
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include DESeq2 normalized values for each Sample
Supplementary files format and content: Bedgraph file

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) followed by DNAseI treatment (Qiagen) and a cleanup with RNeasy MinElute Cleanup Kit (Qiagen). RNA quality and integrity was confirmed with an Agilent Tapestation (Agilent)
Sequencing libraries were generated using the Illumina Stranded mRNA Prep kit

value: transduced with pBABE-JUNB and selected in 1 microgram/ml puromycin


title: CUT&RUN sequencing of A375 cells (TRIM28 antibody) [TRIM28]

value: permeablized with digitonin, incubated with ITRIM28 antibody, followed by DNA digestion with pAG-MNase


title: A375 cells transduced with pBABE-JUNB retrovirus [JUNB_3]


title: RMB2862


title: A375 cells transduced with pBABE-JUNB retrovirus [JUNB_1]


title: A375 cells transduced with pBABE-FOSL1 retrovirus [FOSL1_3]

value: transduced with pBABE-FOSL1 and selected in 1 microgram/ml puromycin


title: RMB2861


title: RMB2859


title: A375 cells transduced with pBABE-FOSL1 retrovirus [FOSL1_1]


title: A375 cells transduced with empty vector pBABE retrovirus [EV_4]

value: transduced with pBABE retrovirus and selected in 1 microgram/ml puromycin


title: RMB2860


title: A375 cells transduced with empty vector pBABE retrovirus [EV_3]


title: RMB2858


title: RMB2857


title: A375 cells transduced with empty vector pBABE retrovirus [EV_2]


title: RMB2866


title: A375 cells transduced with pBABE-JUNB retrovirus [JUNB_4]


title: RMB2856


title: RMB2865


title: RMB2855


title: RMB2863


title: A375 cells transduced with empty vector pBABE retrovirus [EV_1]


title: A375 cells transduced with pBABE-FOSL1 retrovirus [FOSL1_2]


title: RMB2851


title: RMB2852


title: RMB2853


title: A375 cells transduced with pBABE-FOSL1 retrovirus [FOSL1_4]


title: RMB2850


title: Lung iNKT_CD244Posi_3

city: Suita

first: TAISAKU

last: OGAWA

state: Osaka

address: 6-2-3 Furuedai

institute: RIKEN

description: rep1-3: independent library preparations;

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each was counted, which provides the number of molecules detected for each gene
The copy number of RNA moelcules per cell for each gene is calculated based on spike-in RNA detection efficiency
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA moelcules per cell for each gene is listed.

source_name: Lung iNKT cell

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: One hundred of TCRbeta+NK1.1+CD1d tet+CD244+CXCR6+ or TCRbeta+NK1.1+CD1d tet+CD244-CXCR6+ iNKT cells were isolated from thymus and lung using FACS cell sorter

tag: markers

value: TCRbeta+NK1.1+CD1d tet+CD244+CXCR6+

value: Lung iNKT cell


title: Lung iNKT_CD244Nega_3

value: TCRbeta+NK1.1+CD1d tet+CD244-CXCR6+


title: Lung iNKT_CD244Nega_2


title: RMB2849


title: Thymus iNKT_CD244Nega_2

source_name: Thymus iNKT cell

value: Thymus iNKT cell


title: Lung iNKT_CD244Posi_1


title: RMB2848


title: Thymus iNKT_CD244Nega_3


title: RMB2854


title: Lung iNKT_CD244Posi_2


title: RMB2847


title: RMB2846


title: RMB2845

value: Adult


title: Thymus iNKT_CD244Posi_2


title: Thymus iNKT_CD244Posi_3


title: Thymus iNKT_CD244Nega_1


title: Thymus iNKT_CD244Posi_1


title: RMB2843


title: Lung iNKT_CD244Nega_1


title: RMB2842


title: RMB2840


title: RMB2841


title: RMB2839


title: RMB2836


title: RMB2835


title: RMB2838


title: RMB2837


title: RMB2834


title: RMB2844


title: RMB2833


title: RMB2831


title: RMB2832


title: RMB2830


title: RMB2829


title: RMB2828


title: HC-16 colon biopsy week 0

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 10.

label: biotin

source_name: colon biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

value: colon

tag: donor id

tag: visit

value: WEEK I-0

tag: diagnosis

value: healthy control

tag: mucosal healing at week 8

tag: clinical remission at week 8


title: RMB2826


title: HC-14 colon biopsy week 0


title: HC-13 colon biopsy week 0


title: HC-15 colon biopsy week 0


title: HC-6 colon biopsy week 0


title: HC-5 colon biopsy week 0


title: RMB2827


title: HC-7 colon biopsy week 0


title: RMB2825


title: HC-3 colon biopsy week 0


title: HC-11 colon biopsy week 0


title: HC-2 colon biopsy week 0


title: RMB2824


title: HC-17 colon biopsy week 0


title: HC-9 colon biopsy week 0


title: HC-12 colon biopsy week 0


title: HC-10 colon biopsy week 0


title: HC-8 colon biopsy week 0


title: HC-4 colon biopsy week 0


title: HC-18 colon biopsy week 0


title: RMB2823


title: RMB2822


title: CNTO1275UCO3001-101302 colon biopsy week 0

value: ulcerative colitis

value: Placebo IV

value: Y


title: RMB2821


title: RMB2820


title: RMB2819


title: RMB2818


title: RMB2816


title: CNTO1275UCO3001-101250 colon biopsy week 0

value: N


title: RMB2813


title: CNTO1275UCO3001-101212 colon biopsy week 0


title: RMB2812


title: RMB2814


title: RMB2811


title: RMB2815


title: RMB2810


title: CNTO1275UCO3001-101236 colon biopsy week 0


title: HC-1 colon biopsy week 0


title: CNTO1275UCO3001-101196 colon biopsy week 0


title: RMB2809


title: CNTO1275UCO3001-100920 colon biopsy week 0

value: Ustekinumab 130 mg IV


title: CNTO1275UCO3001-100999 colon biopsy week 0


title: CNTO1275UCO3001-100996 colon biopsy week 0


title: CNTO1275UCO3001-101103 colon biopsy week 0


title: CNTO1275UCO3001-100924 colon biopsy week 0


title: CNTO1275UCO3001-100968 colon biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)


title: RMB2817


title: CNTO1275UCO3001-100929 colon biopsy week 0


title: CNTO1275UCO3001-100942 colon biopsy week 0


title: RMB2808


title: RMB2807


title: RMB2804


title: RMB2805


title: CNTO1275UCO3001-101172 colon biopsy week 0


title: RMB2803


title: RMB2802


title: CNTO1275UCO3001-100914 colon biopsy week 0


title: RMB2800


title: RMB2801


title: RMB2806


title: RMB2798


title: CNTO1275UCO3001-100916 colon biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)


title: RMB2799


title: CNTO1275UCO3001-100940 colon biopsy week 0


title: CNTO1275UCO3001-100906 colon biopsy week 0


title: RMB2797


title: CNTO1275UCO3001-100898 colon biopsy week 0


title: CNTO1275UCO3001-100902 colon biopsy week 0


title: RMB2796


title: CNTO1275UCO3001-100899 colon biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: RMB2795


title: RMB2794


title: RMB2793


title: RMB2792


title: CNTO1275UCO3001-100886 colon biopsy week 0


title: RMB2790


title: CNTO1275UCO3001-100882 colon biopsy week 0


title: CNTO1275UCO3001-100891 colon biopsy week 0


title: CNTO1275UCO3001-100895 colon biopsy week 0


title: RMB2791


title: CNTO1275UCO3001-100876 colon biopsy week 0


title: RMB2789


title: CNTO1275UCO3001-100885 colon biopsy week 0


title: CNTO1275UCO3001-100875 colon biopsy week 0


title: CNTO1275UCO3001-100894 colon biopsy week 0


title: RMB2788


title: CNTO1275UCO3001-100871 colon biopsy week 0


title: RMB2787


title: RMB2786


title: CNTO1275UCO3001-100904 colon biopsy week 0


title: CNTO1275UCO3001-100870 colon biopsy week 0


title: CNTO1275UCO3001-100881 colon biopsy week 0


title: RMB2785


title: CNTO1275UCO3001-100857 colon biopsy week 0


title: CNTO1275UCO3001-100856 colon biopsy week 0


title: CNTO1275UCO3001-100855 colon biopsy week 0


title: CNTO1275UCO3001-100854 colon biopsy week 0


title: CNTO1275UCO3001-100866 colon biopsy week 0


title: RMB2784


title: CNTO1275UCO3001-100852 colon biopsy week 0


title: CNTO1275UCO3001-100847 colon biopsy week 0


title: RMB2783


title: CNTO1275UCO3001-100846 colon biopsy week 0


title: RMB2782


title: RMB2781


title: RMB2780


title: RMB2778


title: RMB2779


title: RMB2777


title: RMB2775


title: RMB2776


title: RMB2772


title: RMB2773


title: RMB2771


title: RMB2770


title: RMB2769


title: CNTO1275UCO3001-100831 colon biopsy week 0


title: CNTO1275UCO3001-100807 colon biopsy week 0


title: RMB2768


title: CNTO1275UCO3001-100804 colon biopsy week 0


title: RMB2774


title: CNTO1275UCO3001-100805 colon biopsy week 0


title: CNTO1275UCO3001-100811 colon biopsy week 0


title: CNTO1275UCO3001-100806 colon biopsy week 0


title: CNTO1275UCO3001-100816 colon biopsy week 0


title: CNTO1275UCO3001-100839 colon biopsy week 0


title: CNTO1275UCO3001-100840 colon biopsy week 0


title: RMB2766


title: CNTO1275UCO3001-100823 colon biopsy week 0


title: CNTO1275UCO3001-100792 colon biopsy week 0


title: CNTO1275UCO3001-100794 colon biopsy week 0


title: CNTO1275UCO3001-100795 colon biopsy week 0


title: CNTO1275UCO3001-100815 colon biopsy week 0


title: CNTO1275UCO3001-100779 colon biopsy week 0


title: RMB2764


title: RMB2767


title: CNTO1275UCO3001-100798 colon biopsy week 0


title: RMB2762


title: RMB2761


title: RMB2759


title: RMB2763


title: RMB2760


title: RMB2765


title: RMB2758


title: RMB2756


title: RMB2755


title: RMB2757


title: RMB2754


title: CNTO1275UCO3001-100778 colon biopsy week 0


title: CNTO1275UCO3001-100773 colon biopsy week 0


title: CNTO1275UCO3001-100762 colon biopsy week 0


title: CNTO1275UCO3001-100769 colon biopsy week 0


title: CNTO1275UCO3001-100767 colon biopsy week 0


title: CNTO1275UCO3001-100758 colon biopsy week 0


title: CNTO1275UCO3001-100759 colon biopsy week 0


title: CNTO1275UCO3001-100748 colon biopsy week 0


title: RMB2753


title: CNTO1275UCO3001-100755 colon biopsy week 0


title: CNTO1275UCO3001-100777 colon biopsy week 0


title: RMB2752


title: CNTO1275UCO3001-100756 colon biopsy week 0


title: CNTO1275UCO3001-100747 colon biopsy week 0


title: RMB2750


title: CNTO1275UCO3001-100745 colon biopsy week 0


title: RMB2749


title: CNTO1275UCO3001-100757 colon biopsy week 0


title: CNTO1275UCO3001-100718 colon biopsy week 0


title: CNTO1275UCO3001-100738 colon biopsy week 0


title: CNTO1275UCO3001-100739 colon biopsy week 0


title: CNTO1275UCO3001-100741 colon biopsy week 0


title: RMB2747


title: RMB2751


title: CNTO1275UCO3001-100714 colon biopsy week 0


title: CNTO1275UCO3001-100715 colon biopsy week 0


title: RMB2745


title: RMB2746


title: RMB2744


title: CNTO1275UCO3001-100716 colon biopsy week 0


title: RMB2743


title: RMB2741


title: CNTO1275UCO3001-100710 colon biopsy week 0


title: CNTO1275UCO3001-100707 colon biopsy week 0


title: RMB2748


title: RMB2742


title: RMB2740


title: CNTO1275UCO3001-100705 colon biopsy week 0


title: RMB2738


title: RMB2737


title: RMB2739


title: RMB2736


title: RMB2735


title: RMB2733


title: RMB2734


title: RMB2730


title: RMB2732


title: RMB2731


title: CNTO1275UCO3001-100701 colon biopsy week 0


title: CNTO1275UCO3001-100703 colon biopsy week 0


title: RMB2729


title: RMB2727


title: RMB2728


title: CNTO1275UCO3001-100704 colon biopsy week 0


title: RMB2726


title: CNTO1275UCO3001-100702 colon biopsy week 0


title: CNTO1275UCO3001-100694 colon biopsy week 0


title: CNTO1275UCO3001-100696 colon biopsy week 0


title: CNTO1275UCO3001-100699 colon biopsy week 0


title: CNTO1275UCO3001-100686 colon biopsy week 0


title: RMB2725


title: CNTO1275UCO3001-100698 colon biopsy week 0


title: CNTO1275UCO3001-100700 colon biopsy week 0


title: CNTO1275UCO3001-100682 colon biopsy week 0


title: RMB2724


title: RMB2723


title: CNTO1275UCO3001-100690 colon biopsy week 0


title: CNTO1275UCO3001-100685 colon biopsy week 0


title: CNTO1275UCO3001-100673 colon biopsy week 0


title: CNTO1275UCO3001-100678 colon biopsy week 0


title: CNTO1275UCO3001-100688 colon biopsy week 0


title: RMB2722


title: CNTO1275UCO3001-100680 colon biopsy week 0


title: RMB2720


title: CNTO1275UCO3001-100672 colon biopsy week 0


title: CNTO1275UCO3001-100679 colon biopsy week 0


title: CNTO1275UCO3001-100665 colon biopsy week 0


title: RMB2719


title: RMB2718


title: RMB2717


title: CNTO1275UCO3001-100671 colon biopsy week 0


title: CNTO1275UCO3001-100662 colon biopsy week 0


title: RMB2721


title: CNTO1275UCO3001-100654 colon biopsy week 0


title: RMB2712


title: CNTO1275UCO3001-100657 colon biopsy week 0


title: RMB2709


title: CNTO1275UCO3001-100663 colon biopsy week 0


title: RMB2708


title: CNTO1275UCO3001-100658 colon biopsy week 0


title: RMB2716


title: RMB2707


title: RMB2714


title: RMB2713


title: RMB2715


title: RMB2706


title: CNTO1275UCO3001-100664 colon biopsy week 0


title: CNTO1275UCO3001-100648 colon biopsy week 0


title: CNTO1275UCO3001-100644 colon biopsy week 0


title: CNTO1275UCO3001-100650 colon biopsy week 0


title: CNTO1275UCO3001-100660 colon biopsy week 0


title: CNTO1275UCO3001-100652 colon biopsy week 0


title: CNTO1275UCO3001-100643 colon biopsy week 0


title: CNTO1275UCO3001-100641 colon biopsy week 0


title: CNTO1275UCO3001-100640 colon biopsy week 0


title: RMB2711


title: RMB2705


title: RMB2704


title: RMB2703


title: RMB2702


title: CNTO1275UCO3001-100638 colon biopsy week 0


title: RMB2701


title: CNTO1275UCO3001-100639 colon biopsy week 0


title: RMB2700


title: RMB2698


title: RMB2696


title: RMB2695


title: RMB2697


title: CNTO1275UCO3001-100635 colon biopsy week 0


title: RMB2693


title: RMB2694


title: CNTO1275UCO3001-100637 colon biopsy week 0


title: RMB2692


title: RMB2699


title: CNTO1275UCO3001-100633 colon biopsy week 0


title: RMB2691


title: CNTO1275UCO3001-100630 colon biopsy week 0


title: CNTO1275UCO3001-100631 colon biopsy week 0


title: CNTO1275UCO3001-100636 colon biopsy week 0


title: CNTO1275UCO3001-100623 colon biopsy week 0


title: CNTO1275UCO3001-100632 colon biopsy week 0


title: RMB2690


title: CNTO1275UCO3001-100627 colon biopsy week 0


title: RMB2689


title: CNTO1275UCO3001-100622 colon biopsy week 0


title: CNTO1275UCO3001-100615 colon biopsy week 0


title: CNTO1275UCO3001-100625 colon biopsy week 0


title: CNTO1275UCO3001-100624 colon biopsy week 0


title: RMB2688


title: CNTO1275UCO3001-100617 colon biopsy week 0


title: RMB2685


title: CNTO1275UCO3001-100616 colon biopsy week 0


title: RMB2687


title: RMB2686


title: CNTO1275UCO3001-100610 colon biopsy week 0


title: RMB2683


title: RMB2682


title: RMB2684


title: CNTO1275UCO3001-100609 colon biopsy week 0


title: CNTO1275UCO3001-100612 colon biopsy week 0


title: CNTO1275UCO3001-100607 colon biopsy week 0


title: RMB2681


title: CNTO1275UCO3001-100608 colon biopsy week 0


title: RMB2678


title: RMB2680


title: RMB2677


title: CNTO1275UCO3001-100605 colon biopsy week 0


title: CNTO1275UCO3001-100651 colon biopsy week 0


title: CNTO1275UCO3001-100604 colon biopsy week 0


title: CNTO1275UCO3001-100598 colon biopsy week 0


title: CNTO1275UCO3001-100603 colon biopsy week 0


title: RMB2676


title: CNTO1275UCO3001-100597 colon biopsy week 0


title: CNTO1275UCO3001-100596 colon biopsy week 0


title: RMB2675


title: CNTO1275UCO3001-100595 colon biopsy week 0


title: CNTO1275UCO3001-100594 colon biopsy week 0


title: RMB2674


title: RMB2673


title: CNTO1275UCO3001-100593 colon biopsy week 0


title: RMB2679


title: RMB2672


title: RMB2671


title: RMB2667


title: RMB2670


title: RMB2669


title: RMB2668


title: RMB2666


title: RMB2664


title: RMB2665


title: CNTO1275UCO3001-100585 colon biopsy week 0


title: RMB2663


title: CNTO1275UCO3001-100584 colon biopsy week 0


title: CNTO1275UCO3001-100592 colon biopsy week 0


title: RMB2661


title: RMB2710


title: RMB2662


title: CNTO1275UCO3001-100583 colon biopsy week 0


title: RMB2660


title: CNTO1275UCO3001-100582 colon biopsy week 0


title: CNTO1275UCO3001-100573 colon biopsy week 0


title: CNTO1275UCO3001-100566 colon biopsy week 0


title: CNTO1275UCO3001-100579 colon biopsy week 0


title: CNTO1275UCO3001-100574 colon biopsy week 0


title: RMB2659


title: CNTO1275UCO3001-100578 colon biopsy week 0


title: RMB2658


title: CNTO1275UCO3001-100572 colon biopsy week 0


title: CNTO1275UCO3001-100571 colon biopsy week 0


title: CNTO1275UCO3001-100559 colon biopsy week 0


title: CNTO1275UCO3001-100568 colon biopsy week 0


title: CNTO1275UCO3001-100563 colon biopsy week 0


title: CNTO1275UCO3001-100646 colon biopsy week 0


title: CNTO1275UCO3001-100556 colon biopsy week 0


title: CNTO1275UCO3001-100565 colon biopsy week 0


title: RMB2656


title: RMB2654


title: RMB2653


title: RMB2657


title: RMB2652


title: RMB2650


title: RMB2649


title: RMB2655


title: RMB2651


title: CNTO1275UCO3001-100555 colon biopsy week 0


title: RMB2646


title: RMB2648


title: CNTO1275UCO3001-100549 colon biopsy week 0


title: RMB2647


title: RMB2645


title: RMB2644


title: CNTO1275UCO3001-100553 colon biopsy week 0


title: CNTO1275UCO3001-100548 colon biopsy week 0


title: RMB2643


title: CNTO1275UCO3001-100546 colon biopsy week 0


title: CNTO1275UCO3001-100554 colon biopsy week 0


title: CNTO1275UCO3001-100543 colon biopsy week 0


title: CNTO1275UCO3001-100545 colon biopsy week 0


title: CNTO1275UCO3001-100539 colon biopsy week 0


title: CNTO1275UCO3001-100541 colon biopsy week 0


title: CNTO1275UCO3001-100537 colon biopsy week 0


title: CNTO1275UCO3001-100538 colon biopsy week 0


title: CNTO1275UCO3001-100544 colon biopsy week 0


title: CNTO1275UCO3001-100540 colon biopsy week 0


title: RMB2642


title: RMB2641


title: RMB2640


title: RMB2638


title: RMB2639


title: RMB2637


title: RMB2636


title: RMB2635


title: RMB2634


title: RMB2633


title: CNTO1275UCO3001-100533 colon biopsy week 0


title: CNTO1275UCO3001-100534 colon biopsy week 0


title: CNTO1275UCO3001-100532 colon biopsy week 0


title: CNTO1275UCO3001-100531 colon biopsy week 0


title: CNTO1275UCO3001-100527 colon biopsy week 0


title: CNTO1275UCO3001-100528 colon biopsy week 0


title: RMB2631


title: CNTO1275UCO3001-100525 colon biopsy week 0


title: CNTO1275UCO3001-100521 colon biopsy week 0


title: RMB2630


title: RMB2628


title: RMB2627


title: RMB2629


title: CNTO1275UCO3001-100516 colon biopsy week 0


title: RMB2626


title: RMB2625


title: RMB2624


title: RMB2623


title: RMB2621


title: CNTO1275UCO3001-100517 colon biopsy week 0


title: RMB2622


title: CNTO1275UCO3001-100515 colon biopsy week 0


title: CNTO1275UCO3001-100509 colon biopsy week 0


title: CNTO1275UCO3001-100513 colon biopsy week 0


title: RMB2620


title: RMB2632


title: CNTO1275UCO3001-100518 colon biopsy week 0


title: RMB2617


title: CNTO1275UCO3001-100514 colon biopsy week 0


title: CNTO1275UCO3001-100511 colon biopsy week 0


title: RMB2618


title: CNTO1275UCO3001-100508 colon biopsy week 0


title: CNTO1275UCO3001-100507 colon biopsy week 0


title: CNTO1275UCO3001-100522 colon biopsy week 0


title: CNTO1275UCO3001-100506 colon biopsy week 0


title: CNTO1275UCO3001-100497 colon biopsy week 0


title: CNTO1275UCO3001-100512 colon biopsy week 0


title: CNTO1275UCO3001-100502 colon biopsy week 0


title: CNTO1275UCO3001-100495 colon biopsy week 0


title: CNTO1275UCO3001-100501 colon biopsy week 0


title: CNTO1275UCO3001-100499 colon biopsy week 0


title: RMB2616


title: RMB2619


title: RMB2614


title: RMB2615


title: RMB2612


title: RMB2613


title: CNTO1275UCO3001-100493 colon biopsy week 0


title: RMB2611


title: RMB2610


title: CNTO1275UCO3001-100496 colon biopsy week 0


title: RMB2607


title: CNTO1275UCO3001-100488 colon biopsy week 0


title: CNTO1275UCO3001-100480 colon biopsy week 0


title: RMB2604


title: CNTO1275UCO3001-100472 colon biopsy week 0


title: RMB2603


title: CNTO1275UCO3001-100473 colon biopsy week 0


title: CNTO1275UCO3001-100479 colon biopsy week 0


title: RMB2606


title: CNTO1275UCO3001-100483 colon biopsy week 0


title: CNTO1275UCO3001-100494 colon biopsy week 0


title: CNTO1275UCO3001-100468 colon biopsy week 0


title: RMB2602


title: RMB2601


title: CNTO1275UCO3001-100486 colon biopsy week 0


title: CNTO1275UCO3001-100465 colon biopsy week 0


title: RMB2609


title: RMB2605


title: RMB2599


title: CNTO1275UCO3001-100463 colon biopsy week 0


title: CNTO1275UCO3001-100461 colon biopsy week 0


title: RMB2598


title: CNTO1275UCO3001-100457 colon biopsy week 0


title: CNTO1275UCO3001-100460 colon biopsy week 0


title: CNTO1275UCO3001-100455 colon biopsy week 0


title: CNTO1275UCO3001-100467 colon biopsy week 0


title: RMB2600


title: RMB2594


title: RMB2597


title: RMB2595


title: RMB2596


title: CNTO1275UCO3001-100454 colon biopsy week 0


title: RMB2592


title: CNTO1275UCO3001-100462 colon biopsy week 0


title: RMB2593


title: RMB2591


title: RMB2608


title: RMB2589


title: CNTO1275UCO3001-100453 colon biopsy week 0


title: RMB2588


title: CNTO1275UCO3001-100451 colon biopsy week 0


title: CNTO1275UCO3001-100448 colon biopsy week 0


title: CNTO1275UCO3001-100449 colon biopsy week 0


title: CNTO1275UCO3001-100450 colon biopsy week 0


title: CNTO1275UCO3001-100445 colon biopsy week 0


title: CNTO1275UCO3001-100446 colon biopsy week 0


title: CNTO1275UCO3001-100441 colon biopsy week 0


title: CNTO1275UCO3001-100447 colon biopsy week 0


title: CNTO1275UCO3001-100438 colon biopsy week 0


title: RMB2585


title: CNTO1275UCO3001-100452 colon biopsy week 0


title: RMB2584


title: CNTO1275UCO3001-100444 colon biopsy week 0


title: RMB2583


title: RMB2582


title: RMB2590


title: RMB2581


title: CNTO1275UCO3001-100436 colon biopsy week 0


title: CNTO1275UCO3001-100437 colon biopsy week 0


title: RMB2587


title: RMB2580


title: RMB2586


title: CNTO1275UCO3001-100443 colon biopsy week 0


title: CNTO1275UCO3001-100431 colon biopsy week 0


title: CNTO1275UCO3001-100435 colon biopsy week 0


title: CNTO1275UCO3001-100433 colon biopsy week 0


title: CNTO1275UCO3001-100429 colon biopsy week 0


title: CNTO1275UCO3001-100430 colon biopsy week 0


title: RMB2578


title: RMB2577


title: RMB2576


title: RMB2575


title: CNTO1275UCO3001-100427 colon biopsy week 0


title: RMB2572


title: RMB2573


title: RMB2574


title: CNTO1275UCO3001-100426 colon biopsy week 0


title: RMB2571


title: RMB2579


title: RMB2569


title: CNTO1275UCO3001-100419 colon biopsy week 0


title: CNTO1275UCO3001-100418 colon biopsy week 0


title: CNTO1275UCO3001-100421 colon biopsy week 0


title: RMB2568


title: CNTO1275UCO3001-100425 colon biopsy week 0


title: CNTO1275UCO3001-100420 colon biopsy week 0


title: RMB2567


title: CNTO1275UCO3001-100423 colon biopsy week 0


title: RMB2570


title: RMB2566


title: CNTO1275UCO3001-100416 colon biopsy week 0


title: RMB2565


title: RMB2563


title: RMB2564


title: RMB2562


title: RMB2560


title: RMB2561


title: CNTO1275UCO3001-100415 colon biopsy week 0


title: CNTO1275UCO3001-100414 colon biopsy week 0


title: CNTO1275UCO3001-100410 colon biopsy week 0


title: CNTO1275UCO3001-100409 colon biopsy week 0


title: CNTO1275UCO3001-100412 colon biopsy week 0


title: CNTO1275UCO3001-100413 colon biopsy week 0


title: CNTO1275UCO3001-100411 colon biopsy week 0


title: RMB2556


title: RMB2557


title: RMB2559


title: RMB2555


title: CNTO1275UCO3001-100406 colon biopsy week 0


title: RMB2554


title: RMB2551


title: RMB2558


title: RMB2550


title: RMB2549


title: CNTO1275UCO3001-100408 colon biopsy week 0


title: RMB2553


title: CNTO1275UCO3001-100398 colon biopsy week 0


title: CNTO1275UCO3001-100397 colon biopsy week 0


title: CNTO1275UCO3001-100403 colon biopsy week 0


title: CNTO1275UCO3001-100404 colon biopsy week 0


title: CNTO1275UCO3001-100399 colon biopsy week 0


title: CNTO1275UCO3001-100395 colon biopsy week 0


title: CNTO1275UCO3001-100393 colon biopsy week 0


title: RMB2548


title: RMB2547


title: RMB2545


title: CNTO1275UCO3001-100396 colon biopsy week 0


title: RMB2546


title: scRNAseq_patient_3_adjacent

status: Public on Aug 12 2022

city: New York

first: John

last: Grout

state: NY

address: 50 east 98th, apt. 11a4

institute: Mount Sinai School of Medicine

data_processing:
Cell Ranger 3 for demultiplexing, alignment and cell counting.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

extract_protocol:
Stromal cells were sorted using a combination of positive and negative gating. CD45 and EpCAM were used to remove immune and epithelial/tumor cells respecitvely while CD29 and PDPN were used to positively select for stromal cells.
Library preparation was done according to 10X genomics protocols and their correponding verions as listed below.
ssRNA-seq

treatment_protocol: The non-involved adjacent lung and tumor tissue were diced by scissors then enzymatically digested with collagenase and Dnase. Digested tissue was agitated with repeated passes through a syringe and strained through a 70 miron strainer. The single cell suspension was resuspended in PBS until cell sorting.

tag: tissue type

value: Adjacent

tag: disease

value: sorted stromal cells


title: RMB2544

tag: age


title: CNTO1275UCO3001-100388 colon biopsy week 0


title: RMB2543


title: RMB2542


title: CNTO1275UCO3001-100387 colon biopsy week 0


title: CNTO1275UCO3001-100381 colon biopsy week 0


title: CNTO1275UCO3001-100378 colon biopsy week 0


title: CNTO1275UCO3001-100391 colon biopsy week 0


title: CNTO1275UCO3001-100380 colon biopsy week 0


title: RMB2541


title: RMB2540


title: CNTO1275UCO3001-100394 colon biopsy week 0


title: CNTO1275UCO3001-100379 colon biopsy week 0


title: RMB2538


title: RMB2539


title: CNTO1275UCO3001-100376 colon biopsy week 0


title: RMB2537


title: CNTO1275UCO3001-100377 colon biopsy week 0


title: RMB2535


title: RMB2534


title: RMB2536


title: CNTO1275UCO3001-100372 colon biopsy week 0


title: RMB2533


title: CNTO1275UCO3001-100370 colon biopsy week 0


title: CNTO1275UCO3001-100375 colon biopsy week 0


title: CNTO1275UCO3001-100371 colon biopsy week 0


title: RMB2532


title: CNTO1275UCO3001-100368 colon biopsy week 0


title: CNTO1275UCO3001-100369 colon biopsy week 0


title: RMB2531


title: RMB2530


title: RMB2529


title: RMB2528


title: CNTO1275UCO3001-100366 colon biopsy week 0


title: RMB2527


title: RMB2526


title: CNTO1275UCO3001-100373 colon biopsy week 0


title: RMB2525


title: CNTO1275UCO3001-100367 colon biopsy week 0


title: CNTO1275UCO3001-100363 colon biopsy week 0


title: CNTO1275UCO3001-100365 colon biopsy week 0


title: CNTO1275UCO3001-100360 colon biopsy week 0


title: CNTO1275UCO3001-100357 colon biopsy week 0


title: RMB2523


title: CNTO1275UCO3001-100354 colon biopsy week 0


title: RMB2522


title: CNTO1275UCO3001-100362 colon biopsy week 0


title: CNTO1275UCO3001-100356 colon biopsy week 0


title: CNTO1275UCO3001-100355 colon biopsy week 0


title: RMB2521


title: RMB2519


title: RMB2520


title: CNTO1275UCO3001-100353 colon biopsy week 0


title: RMB2552


title: RMB2518


title: RMB2517


title: Control 48

city: LOS ANGELES

first: Neal

last: Yuan

state: CA

address: 8700 Beverly Blvd, Davis 1015

institute: Cedars-Sinai

data_processing: We excluded any miRNA if greater than 80% of samples failed to meet manufacturer quality scores, a sign of either very low miRNA levels and/or failed amplification. We normalized miRNA expression data by subtracting the cycle threshold (Ct) from the global mean across the Ct’s of all miRNAs for that patient, a widely accepted normalization method (see D’haene Methods Mol Biol 2012). Lastly, we excluded any patients if greater than 80% of their samples failed to meet quality scores.

label: EVAGREEN

source_name: platelet poor plasma

extract_protocol: miRNeasy Serum Plasma Kit

tag: condition

value: control


title: RMB2516


title: RMB2524


title: RMB2515


title: RMB2514


title: RMB2513


title: CNTO1275UCO3001-100417 colon biopsy week 0


title: RMB2512


title: RMB2511


title: CNTO1275UCO3001-100352 colon biopsy week 0


title: CNTO1275UCO3001-100345 colon biopsy week 0


title: CNTO1275UCO3001-100351 colon biopsy week 0


title: CNTO1275UCO3001-100346 colon biopsy week 0


title: CNTO1275UCO3001-100349 colon biopsy week 0


title: CNTO1275UCO3001-100344 colon biopsy week 0


title: CNTO1275UCO3001-100343 colon biopsy week 0


title: RMB2510


title: RMB2508


title: RMB2509


title: RMB2506


title: RMB2505


title: CNTO1275UCO3001-100340 colon biopsy week 0


title: RMB2504


title: CNTO1275UCO3001-100341 colon biopsy week 0


title: RMB2503


title: RMB2502


title: RMB2499


title: RMB2507


title: CNTO1275UCO3001-100342 colon biopsy week 0


title: CNTO1275UCO3001-100385 colon biopsy week 0


title: CNTO1275UCO3001-100339 colon biopsy week 0


title: RMB2497


title: CNTO1275UCO3001-100338 colon biopsy week 0


title: CNTO1275UCO3001-100337 colon biopsy week 0


title: CNTO1275UCO3001-100331 colon biopsy week 0


title: CNTO1275UCO3001-100330 colon biopsy week 0


title: CNTO1275UCO3001-100336 colon biopsy week 0


title: RMB2501


title: CNTO1275UCO3001-100335 colon biopsy week 0


title: RMB2500


title: RMB2496


title: RMB2495


title: CNTO1275UCO3001-100327 colon biopsy week 0


title: CNTO1275UCO3001-100319 colon biopsy week 0


title: RMB2494


title: CNTO1275UCO3001-100328 colon biopsy week 0


title: CNTO1275UCO3001-100321 colon biopsy week 0


title: CNTO1275UCO3001-100318 colon biopsy week 0


title: RMB2498


title: RMB2493


title: RMB2492


title: CNTO1275UCO3001-100333 colon biopsy week 0


title: CNTO1275UCO3001-100326 colon biopsy week 0


title: CNTO1275UCO3001-100323 colon biopsy week 0


title: CNTO1275UCO3001-100329 colon biopsy week 0


title: RMB2491


title: CNTO1275UCO3001-100324 colon biopsy week 0


title: RMB2490


title: CNTO1275UCO3001-100316 colon biopsy week 0


title: RMB2489


title: CNTO1275UCO3001-100313 colon biopsy week 0


title: CNTO1275UCO3001-100315 colon biopsy week 0


title: CNTO1275UCO3001-100314 colon biopsy week 0


title: RMB2488


title: RMB2487


title: RMB2486


title: RMB2485


title: RMB2484


title: CNTO1275UCO3001-100312 colon biopsy week 0


title: RMB2483


title: RMB2482


title: RMB2481


title: RMB2480


title: CNTO1275UCO3001-100304 colon biopsy week 0


title: CNTO1275UCO3001-100311 colon biopsy week 0


title: RMB2478


title: CNTO1275UCO3001-100308 colon biopsy week 0


title: CNTO1275UCO3001-100309 colon biopsy week 0


title: CNTO1275UCO3001-100306 colon biopsy week 0


title: CNTO1275UCO3001-100299 colon biopsy week 0


title: RMB2476


title: CNTO1275UCO3001-100293 colon biopsy week 0


title: CNTO1275UCO3001-100294 colon biopsy week 0


title: CNTO1275UCO3001-100291 colon biopsy week 0


title: RMB2475


title: RMB2477


title: RMB2474


title: CNTO1275UCO3001-100305 colon biopsy week 0


title: CNTO1275UCO3001-100296 colon biopsy week 0


title: RMB2473


title: RMB2471


title: CNTO1275UCO3001-100289 colon biopsy week 0


title: RMB2479


title: RMB2469


title: RMB2468


title: CNTO1275UCO3001-100287 colon biopsy week 0


title: CNTO1275UCO3001-100302 colon biopsy week 0


title: CNTO1275UCO3001-100284 colon biopsy week 0


title: CNTO1275UCO3001-100303 colon biopsy week 0


title: CNTO1275UCO3001-100288 colon biopsy week 0


title: RMB2467


title: CNTO1275UCO3001-100283 colon biopsy week 0


title: CNTO1275UCO3001-100282 colon biopsy week 0


title: CNTO1275UCO3001-100281 colon biopsy week 0


title: RMB2472


title: RMB2466


title: CNTO1275UCO3001-100285 colon biopsy week 0


title: CNTO1275UCO3001-100290 colon biopsy week 0


title: RMB2464


title: RMB2463


title: RMB2470


title: RMB2462


title: CNTO1275UCO3001-100280 colon biopsy week 0


title: CNTO1275UCO3001-100279 colon biopsy week 0


title: RMB2460


title: RMB2461


title: CNTO1275UCO3001-100276 colon biopsy week 0


title: CNTO1275UCO3001-100273 colon biopsy week 0


title: CNTO1275UCO3001-100274 colon biopsy week 0


title: CNTO1275UCO3001-100271 colon biopsy week 0


title: CNTO1275UCO3001-100265 colon biopsy week 0


title: RMB2465


title: RMB2459


title: CNTO1275UCO3001-100267 colon biopsy week 0


title: RMB2458


title: RMB2455


title: RMB2454


title: RMB2457


title: RMB2453


title: RMB2456


title: RMB2450


title: RMB2448


title: CNTO1275UCO3001-100264 colon biopsy week 0


title: RMB2447


title: CNTO1275UCO3001-100262 colon biopsy week 0


title: CNTO1275UCO3001-100263 colon biopsy week 0


title: CNTO1275UCO3001-100266 colon biopsy week 0


title: CNTO1275UCO3001-100249 colon biopsy week 0


title: CNTO1275UCO3001-100253 colon biopsy week 0


title: RMB2446


title: CNTO1275UCO3001-100248 colon biopsy week 0


title: CNTO1275UCO3001-100261 colon biopsy week 0


title: CNTO1275UCO3001-100259 colon biopsy week 0


title: CNTO1275UCO3001-100260 colon biopsy week 0


title: RMB2451


title: CNTO1275UCO3001-100256 colon biopsy week 0


title: RMB2443


title: RMB2444


title: RMB2445


title: RMB2442


title: CNTO1275UCO3001-100254 colon biopsy week 0


title: RMB2441


title: RMB2449


title: RMB2440


title: RMB2439


title: RMB2438


title: RMB2437


title: RMB2435


title: RMB2436


title: CNTO1275UCO3001-100246 colon biopsy week 0


title: RMB2434


title: RMB2433


title: CNTO1275UCO3001-100242 colon biopsy week 0


title: RMB2432


title: CNTO1275UCO3001-100236 colon biopsy week 0


title: CNTO1275UCO3001-100233 colon biopsy week 0


title: CNTO1275UCO3001-100238 colon biopsy week 0


title: RMB2431


title: RMB2430


title: CNTO1275UCO3001-100230 colon biopsy week 0


title: CNTO1275UCO3001-100231 colon biopsy week 0


title: CNTO1275UCO3001-100224 colon biopsy week 0


title: RMB2429


title: RMB2428


title: CNTO1275UCO3001-100219 colon biopsy week 0


title: CNTO1275UCO3001-100229 colon biopsy week 0


title: CNTO1275UCO3001-100226 colon biopsy week 0


title: CNTO1275UCO3001-100225 colon biopsy week 0


title: CNTO1275UCO3001-100228 colon biopsy week 0


title: CNTO1275UCO3001-100247 colon biopsy week 0


title: CNTO1275UCO3001-100221 colon biopsy week 0


title: CNTO1275UCO3001-100239 colon biopsy week 0


title: RMB2425


title: CNTO1275UCO3001-100232 colon biopsy week 0


title: CNTO1275UCO3001-100220 colon biopsy week 0


title: CNTO1275UCO3001-100227 colon biopsy week 0


title: RMB2424


title: CNTO1275UCO3001-100218 colon biopsy week 0


title: RMB2423


title: CNTO1275UCO3001-100216 colon biopsy week 0


title: CNTO1275UCO3001-100215 colon biopsy week 0


title: RMB2422


title: RMB2421


title: CNTO1275UCO3001-100212 colon biopsy week 0


title: RMB2426


title: RMB2420


title: CNTO1275UCO3001-100210 colon biopsy week 0


title: RMB2418


title: RMB2419


title: RMB2417


title: RMB2415


title: RMB2414


title: RMB2413


title: RMB2416


title: CNTO1275UCO3001-100208 colon biopsy week 0


title: RMB2411


title: RMB2412


title: RMB2410


title: CNTO1275UCO3001-100213 colon biopsy week 0


title: CNTO1275UCO3001-100206 colon biopsy week 0


title: CNTO1275UCO3001-100202 colon biopsy week 0


title: CNTO1275UCO3001-100211 colon biopsy week 0


title: CNTO1275UCO3001-100201 colon biopsy week 0


title: CNTO1275UCO3001-100195 colon biopsy week 0


title: CNTO1275UCO3001-100194 colon biopsy week 0


title: CNTO1275UCO3001-100197 colon biopsy week 0


title: CNTO1275UCO3001-100205 colon biopsy week 0


title: CNTO1275UCO3001-100203 colon biopsy week 0


title: RMB2408


title: CNTO1275UCO3001-100209 colon biopsy week 0


title: CNTO1275UCO3001-100200 colon biopsy week 0


title: CNTO1275UCO3001-100207 colon biopsy week 0


title: CNTO1275UCO3001-100192 colon biopsy week 0


title: RMB2407


title: RMB2405


title: RMB2404


title: RMB2409


title: RMB2403


title: CNTO1275UCO3001-100191 colon biopsy week 0


title: RMB2402


title: RMB2401


title: RMB2452


title: RMB2400


title: RMB2406


title: RMB2399


title: CNTO1275UCO3001-100186 colon biopsy week 0


title: RMB2397


title: CNTO1275UCO3001-100187 colon biopsy week 0


title: CNTO1275UCO3001-100189 colon biopsy week 0


title: RMB2398


title: RMB2396


title: CNTO1275UCO3001-100185 colon biopsy week 0


title: CNTO1275UCO3001-100184 colon biopsy week 0


title: RMB2395


title: CNTO1275UCO3001-100182 colon biopsy week 0


title: CNTO1275UCO3001-100183 colon biopsy week 0


title: RMB2394


title: RMB2393


title: RMB2392


title: CNTO1275UCO3001-100180 colon biopsy week 0


title: RMB2391


title: CNTO1275UCO3001-100179 colon biopsy week 0


title: CNTO1275UCO3001-100176 colon biopsy week 0


title: CNTO1275UCO3001-100175 colon biopsy week 0


title: CNTO1275UCO3001-100170 colon biopsy week 0


title: RMB2390


title: CNTO1275UCO3001-100172 colon biopsy week 0


title: CNTO1275UCO3001-100174 colon biopsy week 0


title: RMB2388


title: RMB2387


title: RMB2386


title: RMB2385


title: CNTO1275UCO3001-100168 colon biopsy week 0


title: RMB2384


title: RMB2383


title: CNTO1275UCO3001-100181 colon biopsy week 0


title: RMB2389


title: CNTO1275UCO3001-100167 colon biopsy week 0


title: CNTO1275UCO3001-100169 colon biopsy week 0


title: CNTO1275UCO3001-100165 colon biopsy week 0


title: RMB2381


title: RMB2382


title: RMB2380


title: CNTO1275UCO3001-100162 colon biopsy week 0


title: CNTO1275UCO3001-100157 colon biopsy week 0


title: CNTO1275UCO3001-100161 colon biopsy week 0


title: CNTO1275UCO3001-100164 colon biopsy week 0


title: CNTO1275UCO3001-100156 colon biopsy week 0


title: CNTO1275UCO3001-100154 colon biopsy week 0


title: CNTO1275UCO3001-100155 colon biopsy week 0


title: RMB2376


title: CNTO1275UCO3001-100160 colon biopsy week 0


title: RMB2379


title: RMB2377


title: RMB2378


title: CNTO1275UCO3001-100150 colon biopsy week 0


title: RMB2375


title: RMB2374


title: CNTO1275UCO3001-100151 colon biopsy week 0


title: CNTO1275UCO3001-100148 colon biopsy week 0


title: RMB2373


title: RMB2427


title: CNTO1275UCO3001-100145 colon biopsy week 0


title: CNTO1275UCO3001-100146 colon biopsy week 0


title: RMB2370


title: CNTO1275UCO3001-100152 colon biopsy week 0


title: RMB2368


title: CNTO1275UCO3001-100144 colon biopsy week 0


title: CNTO1275UCO3001-100147 colon biopsy week 0


title: CNTO1275UCO3001-100143 colon biopsy week 0


title: RMB2363


title: RMB2366


title: RMB2367


title: CNTO1275UCO3001-100140 colon biopsy week 0


title: CNTO1275UCO3001-100138 colon biopsy week 0


title: CNTO1275UCO3001-100139 colon biopsy week 0


title: CNTO1275UCO3001-100149 colon biopsy week 0


title: CNTO1275UCO3001-100137 colon biopsy week 0


title: RMB2372


title: RMB2364


title: RMB2365


title: RMB2371


title: RMB2362


title: CNTO1275UCO3001-100135 colon biopsy week 0


title: CNTO1275UCO3001-100141 colon biopsy week 0


title: CNTO1275UCO3001-100136 colon biopsy week 0


title: CNTO1275UCO3001-100132 colon biopsy week 0


title: RMB2359


title: CNTO1275UCO3001-100131 colon biopsy week 0


title: CNTO1275UCO3001-100134 colon biopsy week 0


title: RMB2358


title: RMB2360


title: RMB2357


title: RMB2355


title: RMB2353


title: RMB2356


title: RMB2361


title: CNTO1275UCO3001-100130 colon biopsy week 0


title: CNTO1275UCO3001-100129 colon biopsy week 0


title: RMB2354


title: CNTO1275UCO3001-100126 colon biopsy week 0


title: RMB2351


title: CNTO1275UCO3001-100125 colon biopsy week 0


title: CNTO1275UCO3001-100127 colon biopsy week 0


title: RMB2352


title: RMB2369


title: RMB2349


title: RMB2348


title: RMB2350


title: RMB2346


title: CNTO1275UCO3001-100122 colon biopsy week 0


title: RMB2345


title: RMB2344


title: RMB2343


title: CNTO1275UCO3001-100123 colon biopsy week 0


title: CNTO1275UCO3001-100124 colon biopsy week 0


title: CNTO1275UCO3001-100118 colon biopsy week 0


title: CNTO1275UCO3001-100121 colon biopsy week 0


title: RMB2341


title: RMB2340


title: CNTO1275UCO3001-100113 colon biopsy week 0


title: CNTO1275UCO3001-100112 colon biopsy week 0


title: CNTO1275UCO3001-100116 colon biopsy week 0


title: CNTO1275UCO3001-100110 colon biopsy week 0


title: RMB2347


title: CNTO1275UCO3001-100114 colon biopsy week 0


title: CNTO1275UCO3001-100109 colon biopsy week 0


title: CNTO1275UCO3001-100108 colon biopsy week 0


title: CNTO1275UCO3001-100102 colon biopsy week 0


title: CNTO1275UCO3001-100106 colon biopsy week 0


title: RMB2339


title: RMB2338


title: CNTO1275UCO3001-100101 colon biopsy week 0


title: RMB2337


title: RMB2342


title: RMB2336


title: RMB2334


title: RMB2335


title: CNTO1275UCO3001-100111 colon biopsy week 0


title: RMB2333


title: RMB2330


title: CNTO1275UCO3001-100103 colon biopsy week 0


title: CNTO1275UCO3001-100096 colon biopsy week 0


title: RMB2332


title: RMB2331


title: CNTO1275UCO3001-100100 colon biopsy week 0


title: CNTO1275UCO3001-100097 colon biopsy week 0


title: CNTO1275UCO3001-100098 colon biopsy week 0


title: CNTO1275UCO3001-100091 colon biopsy week 0


title: RMB2328


title: RMB2327


title: RMB2329


title: CNTO1275UCO3001-100095 colon biopsy week 0


title: RMB2326


title: RMB2325


title: RMB2324


title: CNTO1275UCO3001-100084 colon biopsy week 0


title: RMB2323


title: CNTO1275UCO3001-100089 colon biopsy week 0


title: CNTO1275UCO3001-100085 colon biopsy week 0


title: CNTO1275UCO3001-100083 colon biopsy week 0


title: CNTO1275UCO3001-100081 colon biopsy week 0


title: RMB2322


title: CNTO1275UCO3001-100082 colon biopsy week 0


title: CNTO1275UCO3001-100078 colon biopsy week 0


title: CNTO1275UCO3001-100092 colon biopsy week 0


title: CNTO1275UCO3001-100076 colon biopsy week 0


title: RMB313


title: RMB312


title: RMB311


title: RMB310


title: RMB309


title: CNTO1275UCO3001-100087 colon biopsy week 0


title: CNTO1275UCO3001-100074 colon biopsy week 0


title: CNTO1275UCO3001-100080 colon biopsy week 0


title: RMB314


title: CNTO1275UCO3001-100069 colon biopsy week 0


title: RMB315


title: RMB307


title: CNTO1275UCO3001-100075 colon biopsy week 0


title: RMB306


title: RMB305


title: CNTO1275UCO3001-100064 colon biopsy week 0


title: CNTO1275UCO3001-100062 colon biopsy week 0


title: RMB304


title: CNTO1275UCO3001-100065 colon biopsy week 0


title: CNTO1275UCO3001-100059 colon biopsy week 0


title: CNTO1275UCO3001-100060 colon biopsy week 0


title: RMB308


title: RMB302


title: CNTO1275UCO3001-100057 colon biopsy week 0


title: RMB299


title: RMB298


title: RMB300


title: CNTO1275UCO3001-100068 colon biopsy week 0


title: CNTO1275UCO3001-100058 colon biopsy week 0


title: CNTO1275UCO3001-100054 colon biopsy week 0


title: CNTO1275UCO3001-100051 colon biopsy week 0


title: RMB297


title: RMB303


title: RMB296


title: CNTO1275UCO3001-100048 colon biopsy week 0


title: CNTO1275UCO3001-100050 colon biopsy week 0


title: RMB301


title: CNTO1275UCO3001-100047 colon biopsy week 0


title: RMB295


title: RMB293


title: CNTO1275UCO3001-100046 colon biopsy week 0


title: RMB294


title: RMB292


title: CNTO1275UCO3001-100040 colon biopsy week 0


title: RMB291


title: RMB288


title: RMB289


title: RMB290


title: RMB287


title: RMB286


title: RMB284


title: RMB282


title: RMB283


title: RMB281


title: CNTO1275UCO3001-100045 colon biopsy week 0


title: CNTO1275UCO3001-100030 colon biopsy week 0


title: CNTO1275UCO3001-100043 colon biopsy week 0


title: CNTO1275UCO3001-100034 colon biopsy week 0


title: RMB280


title: CNTO1275UCO3001-100031 colon biopsy week 0


title: RMB279


title: CNTO1275UCO3001-100037 colon biopsy week 0


title: RMB278


title: RMB285


title: CNTO1275UCO3001-100026 colon biopsy week 0


title: CNTO1275UCO3001-100028 colon biopsy week 0


title: CNTO1275UCO3001-100024 colon biopsy week 0


title: RMB277


title: RMB276


title: CNTO1275UCO3001-100022 colon biopsy week 0


title: RMB275


title: CNTO1275UCO3001-100032 colon biopsy week 0


title: RMB274


title: RMB273


title: CNTO1275UCO3001-100018 colon biopsy week 0


title: CNTO1275UCO3001-100021 colon biopsy week 0


title: CNTO1275UCO3001-100014 colon biopsy week 0


title: CNTO1275UCO3001-100036 colon biopsy week 0


title: RMB271


title: CNTO1275UCO3001-100023 colon biopsy week 0


title: RMB272


title: CNTO1275UCO3001-100013 colon biopsy week 0


title: CNTO1275UCO3001-100015 colon biopsy week 0


title: RMB270


title: CNTO1275UCO3001-100011 colon biopsy week 0


title: CNTO1275UCO3001-100020 colon biopsy week 0


title: RMB269


title: RMB268


title: Cot.smt2.LRFR.03

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Arabidopsis thaliana.TAIR10.39 genome using STAR (v. 2.5.3a)
The number of read counts per gene locus was summarised with htseq-count (v. 0.9.1)(Anders et al., 2015) using Arabidopsis thaliana.TAIR10.39 gene annotation.
Genome_build: Arabidopsis_thaliana.TAIR10.39
Supplementary_files_format_and_content: raw gene counts for every gene in every sample

organism: Arabidopsis thaliana

source_name: Cotyledon, Biorep3

growth_protocol: Seeds were size selected and surface-sterilised using 70% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 3 min followed by 10 min incubation in 100% (v/v) ethanol. Seeds were sowed on 1/2 Murashige and Skoog medium (1⁄2MS) containing 1.6% (w/v) phytoagar (Agar-Agar, plant; Roth) vertical plates and subsequently stratified at 4 °C for 3 day in darkness. Seedlings were grown in 16h/8h, light/dark photoperiod (LD) at 21 °C in a Percival Scientific Model AR-22L (Perry, IA, USA) incubator.

extract_protocol:
For RNA isolation, 5d-old seedlings were harvested in liquid nitrogen and kept in -70 °C for overnight. Next day, seedlings were covered with -70 °C cold RNAlater™-ICE (Thermo Fisher Scientific, United States, AM7030) and transferred to -20 °C for overnight. Cotyledons and hypocotyls are dissected using sharp needles on top of an ice block under a binocular microscope (Nikon, SMZ1500) and RNA isolation is done using RNeasy Mini Kit (Qiagen, Cat. No. / ID: 74004).
For the RNA-sequencing, RNA quality was assessed on a Fragment Analyzer (Agilent Technologies). From 40 ng total RNA, mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module. RNA-seq libraries were then prepared from the mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Massachusetts, USA). Libraries were quantified by a fluorimetric method and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with the resulting libraries using Illumina HiSeq 3000/4000 SR Cluster Kit reagents. Libraries were sequenced on the Illumina HiSeq 4000 with HiSeq 3000/4000 SBS Kit reagents for 150 cycles. Sequencing data were demultiplexed with the bcl2fastq Conversion Software (v. 2.20, Illumina; San Diego, California, USA).

treatment_protocol: WL was emitted from white fluorescence tubes (Lumilux cool white 18W/840) at a fluence rate of 130 μmol m-2s-1 and LRFR was achieved by supplementing WL with 45 μmol m-2s-1 FR light (LEDs) lowering the R (640–700 nm)/FR (700–760 nm) from 1.4 to 0.2, as measured by Ocean Optics USB2000+ spectrometer. The double layer of yellow filter (010 medium yellow, LEE Filters) lowering blue light from 7 μmol m-2s-1 (WL) to 0.5 μmol m-2s-1 (LB) used to cover up the seedlings for LB treatments. Seedlings were grown for 5 days in WL and subsequently kept in WL or transferred to LB or LRFR for additional 3 hours before harvesting for RNA-seq.

value: Cotyledon

value: Low Red/Far-red Light

tag: genotype


title: RMB267

value: Adult


title: CNTO1275UCO3001-100009 colon biopsy week 0

value: colon

tag: treatment


title: Cot.pif457.LRFR.03


title: CNTO1275UCO3001-100007 colon biopsy week 0

value: WEEK I-0


title: RMB266


title: CNTO1275UCO3001-100010 colon biopsy week 0


title: CNTO1275UCO3001-100063 colon biopsy week 0


title: CNTO1275UCO3001-100005 colon biopsy week 0


title: CNTO1275UCO3001-100002 colon biopsy week 0


title: RMB265


title: CNTO1275UCO3001-100004 colon biopsy week 0


title: CNTO1275UCO3001-100008 colon biopsy week 0


title: CNTO1275UCO3001-100001 colon biopsy week 0


title: CNTO1275UCO3001-100003 colon biopsy week 0


title: Cot.Col0.LRFR.03

value: WT


title: Cot.yuc2589.LB.03

value: Low Blue Light


title: Cot.smt2.LB.03


title: RMB263


title: RMB262


title: RMB261


title: RMB260


title: Cot.yuc2589.LRFR.03


title: Cot.Col0.LB.03


title: Cot.smt2.WL.03

value: White Light


title: RMB258


title: RMB259


title: RMB257


title: Cot.Col0.WL.03


title: Cot.yuc2589.WL.03


title: Cot.pif457.LB.03


title: Cot.smt2.LRFR.02

source_name: Cotyledon, Biorep2


title: Cot.pif457.WL.03


title: RMB256


title: Cot.yuc2589.LRFR.02


title: RMB255


title: RMB264


title: RMB254


title: Cot.pif457.LRFR.02


title: RMB253


title: RMB251


title: RMB252


title: RMB250


title: Cot.smt2.LB.02


title: Cot.Col0.LRFR.02


title: RMB249


title: Cot.pif457.LB.02


title: Cot.Col0.LB.02


title: RMB248


title: RMB247


title: Cot.Col0.WL.02


title: Cot.pif457.WL.02


title: RMB244


title: RMB241


title: Cot.yuc2589.WL.02


title: RMB245


title: RMB246


title: RMB242


title: RMB243


title: RMB240


title: Cot.Col0.LRFR.01

source_name: Cotyledon, Biorep1


title: Cot.smt2.LRFR.01


title: Cot.smt2.LB.01


title: Cot.yuc2589.LRFR.01


title: Cot.pif457.LRFR.01


title: Cot.yuc2589.LB.02


title: RMB239


title: RMB238


title: RMB237


title: Cot.smt2.WL.02


title: Cot.Col0.LB.01


title: Cot.smt2.WL.01


title: RMB236


title: Cot.pif457.WL.01


title: RMB234


title: RMB235


title: Cot.Col0.WL.01


title: RMB233


title: RMB232


title: Hyp.smt2.LRFR.03

source_name: Hypocotyl, Biorep3

value: Hypocotyl


title: Cot.yuc2589.LB.01


title: Hyp.yuc2589.LRFR.03


title: RMB230


title: RMB229


title: Hyp.smt2.LB.03


title: Hyp.pif457.LRFR.03


title: Cot.pif457.LB.01


title: Hyp.yuc2589.LB.03


title: Hyp.Col0.LB.03


title: Hyp.Col0.LRFR.03


title: RMB226


title: RMB225


title: RMB227


title: Hyp.pif457.LB.03


title: RMB223


title: RMB224


title: Hyp.yuc2589.WL.03


title: RMB222


title: Hyp.smt2.WL.03


title: Hyp.smt2.LRFR.02

source_name: Hypocotyl, Biorep2


title: Hyp.pif457.WL.03


title: RMB220


title: Cot.yuc2589.WL.01


title: RMB231


title: Hyp.yuc2589.LRFR.02


title: RMB228


title: RMB219


title: Hyp.pif457.LRFR.02


title: RMB216


title: RMB218


title: Hyp.Col0.LRFR.02


title: RMB215


title: RMB217


title: Hyp.smt2.LB.02


title: RMB214


title: Hyp.yuc2589.LB.02


title: RMB212


title: RMB213


title: Hyp.yuc2589.WL.02


title: Hyp.pif457.LB.02


title: Hyp.Col0.WL.03


title: Hyp.smt2.WL.02


title: RMB211


title: RMB210


title: Hyp.Col0.WL.02


title: Hyp.pif457.WL.02


title: RMB209


title: RMB221


title: Hyp.smt2.LRFR.01

source_name: Hypocotyl, Biorep1


title: Hyp.yuc2589.LRFR.01


title: RMB207


title: RMB208


title: RMB206


title: Hyp.pif457.LRFR.01


title: Hyp.Col0.LRFR.01


title: RMB205


title: Hyp.Col0.LB.02


title: RMB204


title: Hyp.yuc2589.LB.01


title: RMB203


title: RMB202


title: RMB201


title: Hyp.pif457.LB.01


title: Hyp.Col0.LB.01


title: RMB200


title: RMB199


title: RMB197


title: RMB196


title: RMB198


title: iPSC IEC, control treatment, replicate 3

city: Wageningen

first: Menno

last: Grouls

address: Postbus 8000

department: Toxicology

country: Netherlands

institute: Wageningen University & Research

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.3.0) was used to map the cleaned reads to the GRCh38.p13 human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release 35). Salmon parameters used: -i ./salmon_index_H35 --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100 --threads 20
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport (version 1.18.0) to estimate gene level counts.
Assembly: GRCm38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates)
Supplementary files format and content: R-object (txi.counts.annotated.GEO.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary files format and content: R object (txi.lengthScaledTPM.annotated.GEO.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

growth_protocol: The human iPSC cell line (CS83iCTR-33n1) was provided by the Cedars-Sinai Medical Center’s David and Janet Polak Foundation Stem Cell Core Laboratory. These cells were established through episomal reprogramming of fibroblasts of a 31-year-old healthy female. The cell line has been fully characterized and no karyotype abnormalities have been found. Undifferentiated human iPSCs were cultured in feeder free conditions using mTeSR1 medium (Stem Cell Technologies, Vancouver, Canada) on human embryonic stem cell qualified matrigel (Corning, New York, NY). For passage, iPSC colonies were dissociated using gentle cell dissociation reagent (Stem Cell Technologies). For differentiation, human iPSCs were dissociated into single cells using accutase (Stem Cell Technologies) and cultured on human embryonic stem cell qualified matrigel-coated 24-well plates in mTeSR1 supplemented with 10 µM Y-27632 (Stem Cell Technologies) for 1 day. Human iPSCs were subsequently differentiated into definitive endoderm (DE) by incubation in RPMI1640 medium containing 1% non-essential amino acids (Gibco) and 100 ng/ml Activin A (Cell Guidance Systems, Cambridge, UK), with increasing concentrations of fetal bovine serum (0%, 0.2% and 2% on day 1, 2 and 3, respectively). 15 ng/ml BMP4 (R&D Systems, Minneapolis, MN) was also added during the first day of definitive endoderm formation. Differentiation into intestinal stem cells was subsequently induced by changing medium into DMEM/F12 containing 2% fetal bovine serum, 1% GlutaMAX (Gibco) and 250ng/ml FGF2 (R&D Systems). After 4 days, cells were dissociated using Accutase and seeded onto polyester transwell inserts (0.4µm, Corning) coated with Growth Factor Reduced matrigel. Cells were cultured for 7 days in intestinal differentiation medium (DMEM/F-12 containing 2% fetal bovine serum, 1% non-essential amino acids (Gibco), 1 × B27 (Gibco), 1 × N2 (Gibco), 1% penicillin/streptomycin (Gibco) and 2 mM l-glutamine (Gibco)) supplemented with 20 ng/ml EGF (R&D Systems) and 1mM 8-Br-cAMP (Sigma). The ROCK inhibitor, y-27632 (10µM; Stem Cell Technologies), was added during the initial 24 hours after seeding to reduce cell death. The cells were subsequently cultured for 12 days in intestinal differentiation medium supplemented with 20 ng/ml EGF, 500uM IBMX (Sigma), 5uM 5-aza-2′-deoxycytidine (Sigma), 20 µM PD98059 (Stem Cell Technologies), and 0.5 µM A-83-01 (Sigma). Medium was refreshed every 2–3 days.

extract_protocol:
Cell were lysed with 350 µL RA1 lysis buffer for 5 min. The entire volume of RA1 solution was collected as cell lysate and total RNA. Total RNA from the iPSC derived IECs was extracted using the NucleoSpin RNA isolation kit (Macherey-Nagel, Duren, Germany) according to manufacturer’s instructions. Quality of the RNA was checked using a NanoDrop One (ThermoFisher, Wilmington, Delaware, USA) and bioanalyzer (Agilent). Samples were sent to BGI (Hong Kong) for transcriptome sequencing using the DNBSEQ Technology Platform with 20M reads per sample.
Library construction and RNA sequencing on DNBSEQ were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: On the last day cells were exposed to sodium-butyrate, sodium-propionate and sodium-acetate (Sigma-Aldrich, Steinheim, Germany) at 1 and 10 mM in triplicate, the same amount of water was added to the medium as a control. After the 24 h incubation the cells were washed with 100 µL DMEM+.

value: iPSC derived intestinal epithelial cells

value: control (water)

tag: time

value: 24 hrs


title: RMB195


title: Hyp.smt2.LB.01

tag: tissue


title: RMB194


title: Hyp.Col0.WL.01


title: Hyp.pif457.WL.01


title: Hyp.yuc2589.WL.01


title: RMB193


title: iPSC IEC, control treatment, replicate 1

tag: cell type


title: iPSC IEC, propionate 10 mM treatment, replicate 3

value: 10 mM NaP [propionic acid sodium salt]


title: iPSC IEC, propionate 10 mM treatment, replicate 2


title: WT, PBS treatment, mouse, rep4

city: Toronto

first: James

middle: J

last: Dowling

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

data_processing:
Sequencing reads were aligned to the mouse(GRCm38) /zebrafish genome(GRCz9) using STAR. Read quality was assessed with FastQC, and adaptors were trimmed from reads using Cutadapt. STAR gene level counts (ReadsPerGene.out.tab files) were used for differential expression with DESeq2 package
Assembly: Zebrafish: GRCz9 / Mus musculus: GRCm38
Supplementary files format and content: tab-delimited text files include the raw count values for each Sample. Rows = genes; Columns = samples.

source_name: tibialis anterior muscle

extract_protocol:
Total RNA was harvested using the Qiagen RNeasy Kit in accordance with the manufacturer’s protocol
Zebrafish: RNA libraries were generated using the QuantSeq 3’ mRNA sequencing kit (Lexogen) automated on an NGS workstation (Agilent)   Mice: RNA libraries were generated using Illumina TruSeq RNA Sample Prep Kit.

value: tibialis anterior muscle

value: PBS treatment


title: Mtm1 KO, PBS treatment, mouse, rep4

value: Mtm1 KO


title: WT, PBS treatment, mouse, rep2


title: WT, PBS treatment, mouse, rep3


title: WT, PBS treatment, mouse, rep1


title: iPSC IEC, propionate 10 mM treatment, replicate 1


title: RMB192


title: Hyp.smt2.WL.01


title: iPSC IEC, propionate 1 mM treatment, replicate 3

value: 1 mM NaP [propionic acid sodium salt]


title: iPSC IEC, propionate 1 mM treatment, replicate 2


title: Mtm1 KO, PBS treatment, mouse, rep3


title: iPSC IEC, acetate 10 mM treatment, replicate 3

value: 10 mM NaA [acetic acid sodium salt]


title: iPSC IEC, propionate 1 mM treatment, replicate 1


title: Mtm1 KO, PBS treatment, mouse, rep2


title: RMB191


title: RMB190


title: iPSC IEC, control treatment, replicate 2


title: iPSC IEC, acetate 10 mM treatment, replicate 2


title: iPSC IEC, acetate 10 mM treatment, replicate 1


title: Mtm1 KO, PBS treatment, mouse, rep1


title: iPSC IEC, acetate 1 mM treatment, replicate 3

value: 1 mM NaA [acetic acid sodium salt]


title: RMB189

value: Adult


title: WT, VPA treatment, mouse, rep4

value: VPA treatment


title: RMB188


title: iPSC IEC, acetate 1 mM treatment, replicate 2


title: RMB187


title: iPSC IEC, butyrate 10 mM treatment, replicate 3

value: 10 mM NaB [butyric acid sodium salt]


title: iPSC IEC, acetate 1 mM treatment, replicate 1

value: WT


title: iPSC IEC, butyrate 10 mM treatment, replicate 1


title: WT, VPA treatment, mouse, rep2


title: iPSC IEC, butyrate 1 mM treatment, replicate 2

value: 1 mM NaB [butyric acid sodium salt]


title: iPSC IEC, butyrate 1 mM treatment, replicate 1


title: iPSC IEC, butyrate 10 mM treatment, replicate 2


title: iPSC IEC, butyrate 1 mM treatment, replicate 3


title: WT, VPA treatment, mouse, rep1


title: RMB185


title: Mtm1 KO, VPA treatment, mouse, rep4


title: Mtm1 KO, VPA treatment, mouse, rep3


title: Tyw1_WT_1_3_repl1

city: Baltimore

first: Jeff

last: Coller

address: 725 N. Wolfe St PCTB 505

institute: Johns Hopkins University

data_processing:
5′ adapter and 3’ CCA and adapter sequences were removed from reads using cutadapt
Reads were mapped with bowtie2 to a yeast tRNA reference generated from GtRNAdb S288c high-confidence mature tRNA fasta file
Read count tables for each isodecoder were produced with Rsubread package’s featureCounts function in R
Reads were summed to generate anticodon-level tables, and both raw reads or RPM tables were obtained for tRNAs grouped by isodecoders or anticodons.
Differential tRNA expression analysis was performed with DESeq2 in R using default settings and p value adjustment (Benjamin–Hochberg correction).
Assembly: S288c
Supplementary files format and content: Csv files that contain RPM for tRNA genes grouped by isodecoders.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown until mid-log phase at 24°C, then collected by centrifugation at 4,000 rpm for 2min.

extract_protocol:
RNA was extracted with Trizol, deacylated and annealed to a double-stranded adapter with RNA ligase 2.
Reverse transcription was performed with Superscript IV, RNA hydrolyzed and the cDNA precipitated then PAGE purified. After precipitation, the cDNA was circularized with CircLigase (Epicentre) and amplified with the NEBnext Ultra II Q5 next-generation master mix. Sequencing was performed as single-end reads for 110 cycles on a NextSeq 550 (v2.5)

value: Budding yeast

tag: strain

value: Mix TYW1:WT RNA 1:3

tag: molecule

value: tRNA


title: RMB184


title: Tyw1_repl1

value: TYW1 deletion


title: Tyw1_repl2


title: RMB183


title: Tyw1_WT_1_3_repl2


title: WT, VPA treatment, mouse, rep3


title: RMB182


title: Tyw1_WT_3_1_repl2

value: Mix TYW1:WT RNA 3:1


title: Mtm1 KO, VPA treatment, mouse, rep2


title: Tyw1_WT_3_1_repl1


title: WT_repl2

source_name: WT


title: Mtm1 KO, VPA treatment, mouse, rep1


title: RMB186


title: RMB180


title: Human_TRPS1C896Y_90days_rep2

type: genomic

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

description:
Hybridized to SNP_6
sample name:
11A_TP1C896Y_rep2

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values were extracted and converted from CEL files to signal intensities using the Copy Number Variation Analysis module of Affymetrix® Genotyping Console 4.2 software.
Processed data file includes: Actual nucleotide indicating the genotype of each SNP; Signal A = signal with first nucleotide; Signal B = signal with second nucleotide.

source_name: MCF-10A cell, TRPS1C896Y, 90days

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from MCF-10A cell preparations using the QIAquick PCR Purification Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Normal breast epithelial cells

tag: cell line

tag: overexpression

value: 90 days


title: WT_repl1


title: Human_TRPS1R908Q_90days_rep1

description:
Hybridized to SNP_6
sample name:
11A_TP1R908Q_rep1

source_name: MCF-10A cell, TRPS1R908Q, 90days


title: Human_TRPS1R908Q_90days_rep2

description:
Hybridized to SNP_6
sample name:
11A_TP1R908Q_rep2


title: Human_TRPS1_90days_rep1

description:
Hybridized to SNP_6
sample name:
11A_TP1_rep1

source_name: MCF-10A cell, TRPS1, 90days


title: 2C-53_S7, srRNAseq

first: Sergey

last: Leikin

state: Maryland

department: NICHD

institute: National Institutes of Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and gene counting were performed with the Space Ranger software (10X Genomics) v1.2.2 (sample 1) and v1.3 (samples 2-6)
Assembly: mm10-2020-A
Supplementary files format and content: *.tiff (original section images), *html (Space Ranger output summary), *.h5 (10X Genomics gene count matrices with tissue location and gene labels), *.jpg (aligned fudicial and detected tissue images), *.json (alignment scale factors), *.png (processed hi and low resolution images of tissue sections), *.csv file (list of tissue locations). Please see ReadMe_and_SeuratInstructions.txt supplementary file for more details and instructions for reading the data into Seurat for analysis.

source_name: tibia

extract_protocol:
Cryosections of fresh frozen proximal tibia areas containing growth plate and adjacent trabecular region were deposited on Visium slides and processed for mRNA extraction according to manufacturer's protocol as described in Gorrell et al, Adv Sci, 2022
Libraries were constructed with 10X Genomics Visium kits for fresh frozen tissue sections following the manufacturer's protocol
10X Genomics Visium, Spatial 3' v1

value: tibia


title: Human_TRPS1C896Y_90days_rep1

description:
Hybridized to SNP_6
sample name:
11A_TP1C896Y_rep1


title: RMB179


title: Human_control_90days_rep2

description:
Hybridized to SNP_6
sample name:
10A_ctr_rep2

source_name: MCF-10A cell, control, 90days

value: control


title: Human_control_90days_rep1

description:
Hybridized to SNP_6
sample name:
10A_ctr_rep1


title: 1D-33_S4, srRNAseq

description: 10x Genomics


title: Human_TRPS1C896Y_30days

description:
Hybridized to SNP_6
sample name:
11A_TP1C896Y

source_name: MCF-10A cell, TRPS1C896Y, 30days

value: 30 days


title: RMB178


title: 1C-33_S3, srRNAseq

description: 10x Genomics


title: 2B-53_S6, srRNAseq

description: 10x Genomics

value: Het G610C


title: RMB175


title: RMB177


title: Human_TRPS1R908Q_30days

description:
Hybridized to SNP_6
sample name:
11A_TP1R908Q

source_name: MCF-10A cell, TRPS1R908Q, 30days


title: 1B-33_S2, srRNAseq

description: 10x Genomics


title: RMB181


title: SL-B_S1, srRNAseq

description: 10x Genomics


title: Mtm1 KO, DMSO treatment, zebrafish, rep4

organism: Danio rerio

source_name: posterior half of larvae

value: posterior half of larvae

value: Mtm1 KO

value: DMSO treatment


title: RMB176

value: Adult


title: Mtm1 KO, DMSO treatment, zebrafish, rep3


title: Human_control_30days

description:
Hybridized to SNP_6
sample name:
10A_ctr

source_name: MCF-10A cell, control, 30days


title: HET, DMSO treatment, zebrafish, rep5

value: HET


title: Human_TRPS1_30days

description:
Hybridized to SNP_6
sample name:
11A_TP1

source_name: MCF-10A cell, TRPS1, 30days


title: Human_TRPS1_90days_rep2

description:
Hybridized to SNP_6
sample name:
11A_TP1_rep2


title: RMB174


title: DC3

city: Nantong

first: He

last: Lichun

address: 9 Seyuan Road

institute: Nantong University

data_processing:
The quality of Illumina raw reads was controlled
Data of fastq format after quality control were processed by Trimmomatic (v0.30) to be high quality clean data.
hen clean data were aligned to reference genome via Hisat2 software (v2.0.1).
Cuffcompare program from Cufflinks v2.2.1 [19] was utilized to identify known transcripts, and novel transcripts, new exonic regions of known genes, and structural optimization of known genes were predicted according to the results from Cuffcompare.
The gene expression level was calculated using FPKM (fragments per kilo bases per Million reads) method
Assembly: 89.38 GRCm38.89
Supplementary files format and content: mapping_stat.txt files include mapping results of each sample
Supplementary files format and content: all.fpkm_anno.xls include FPKM values for each sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated from three random frozen hippocampus samples from the same strain, using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®). Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: hippocampus


title: DC2


title: HET, DMSO treatment, zebrafish, rep4


title: RMB172


title: RMB171


title: HET, DMSO treatment, zebrafish, rep1


title: BC2


title: Mtm1 KO, VPA treatment, zebrafish, rep5

value: VPA treatment


title: RMB170


title: RMB169


title: Mtm1 KO, VPA treatment, zebrafish, rep4


title: Mtm1 KO, VPA treatment, zebrafish, rep2


title: Mtm1 KO, VPA treatment, zebrafish, rep1


title: Mtm1 KO, VPA treatment, zebrafish, rep3


title: RMB168


title: HET, VPA treatment, zebrafish, rep5


title: Mtm1 KO, DMSO treatment, zebrafish, rep2


title: Mtm1 KO, DMSO treatment, zebrafish, rep1


title: RMB173


title: RMB167


title: HET, VPA treatment, zebrafish, rep2


title: RMB166


title: HET, VPA treatment, zebrafish, rep3


title: TRUC Colitis TRUC_5

description: TRUC Colitis

data_processing:
Sequencing reads were trimmed and filtered to remove adaptor contamination and poor-quality bases using trimmomatic.
The resulting read files were mapped to the GRCm38 genome assembly using Hisat2 with default parameters.
The number of reads mapping to the genomic features annotated in Ensembl with a MAPQ score higher than or equal to 10 was calculated using htseq-count with default parameters.
Assembly: GRCm38
Supplementary files format and content: Text file in comma-separated value format with the raw counts of read pairs uniquely and concordantly mapped to each gene

source_name: colon

extract_protocol:
Colon segments were taken from mice after confirmation of death, and placed into 1 ml of RNA later. RNA was extracted from colon segments or purified cells with Qiazol reagent (Invitrogen). In this method, distilled solutions of RNA were purified using chloroform and isopropanol and eluted with ethanol before being resuspended in RNAse free water. RNA was cleaned up using the Qiagen RNeasy Microkit and performing the DNA clean up protocol as listed in the manufacturer’s guidelines. RNA samples were then checked for the quality, contamination and concentration using a NanoDrop, Qubit spectrophotometer and Bioanalyzer. RNA with only a RIN score of above 7 were used for RNA sequencing. RNA was then stored at -80°C awaiting further analysis.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with hairpin loop structure were ligated. The library fragments were then purified with AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: 3% DSS (MW 36,00-50,000, MP Biomedicals, LLC) was administered orally in drinking water for 5 days, DSS was then removed and put back on normal water and mice were culled at day 10 upon recovery. 200μl of 3mg DNBS (Sigma-Aldrich) resolved in 50% EtOH were administered rectally while mice were under isoflurane anaesthesia. 50ug of anti-CD40 (2bScientific, UK) agonist was injected intraperitoneally and mice were culled after 7 days. CD4+ T cells with naive markers (CD4+ CD25- CD44low CD62Lhigh) were sorted using a FACS Aria to a purity of >95%. Rag2-/- mice were injected intraperitoneally with 0.5x10^6 CD4+ cells per mouse and humanely culled after 6-8 weeks. 750ug of anti-IL-10R (2bScientific, UK) were injected into mice intraperitoneally and mice were culled after 4 weeks (unless signs of colitis were seen before).

value: colon

value: Balb/C Tbx21-/- x Rag2-/-

tag: identifier in_raw_counts.csv


title: TRUC Colitis TRUC_4

description: TRUC Colitis


title: TRUC Colitis TRUC_3

description: TRUC Colitis


title: BC3


title: HET, VPA treatment, zebrafish, rep1


title: HET, DMSO treatment, zebrafish, rep2


title: HET, DMSO treatment, zebrafish, rep3


title: TRUC Colitis TRUC_2

description: TRUC Colitis


title: Mtm1 KO, TSA treatment, zebrafish, rep5

value: TSA treatment


title: Mtm1 KO, TSA treatment, zebrafish, rep4


title: untreated Rag2 KO Balb/C Rag2BCR4

description: untreated Rag2 KO Balb/C

value: Balb/C Rag2-/-


title: BC1


title: Mtm1 KO, TSA treatment, zebrafish, rep3


title: RMB164

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 downloaded from GENCODE using RSEM program version 1.2.19 with default parameters.
Gene expression values in transcripts per million (TPM) were calculated using the RSEM program and the mouse GENCODE gene annotation version M4.
Quality control and outlier cell detection was performed using Seurat R package.
Assembly: GRCm38
Supplementary files format and content: tab delimited TPM table

extract_protocol:
single cells were captured on Fluidigm C1 mRNA Seq IFC and lysed and reverse-transcribed in situ
Nextera XT


title: Mtm1 KO, TSA treatment, zebrafish, rep2


title: HET, TSA treatment, zebrafish, rep4


title: RMB163


title: HET, VPA treatment, zebrafish, rep4


title: Mtm1 KO, TSA treatment, zebrafish, rep1


title: HET, TSA treatment, zebrafish, rep3


title: untreated Rag2 KO Balb/C Rag2BCR2

description: untreated Rag2 KO Balb/C


title: untreated Rag2 KO Balb/C Rag2BCR1

description: untreated Rag2 KO Balb/C


title: Balb/C treated with IL10 antibodies IL10_4

description: Balb/C treated with IL10 antibodies

value: Balb/C

value: IL10 blocking antibody


title: RMB162


title: RMB160


title: WT, DMSO treatment, zebrafish, rep3

value: WT


title: WT, DMSO treatment, zebrafish, rep5


title: WT, DMSO treatment, zebrafish, rep2


title: Balb/C treated with IL10 antibodies IL10_2

description: Balb/C treated with IL10 antibodies


title: HET, TSA treatment, zebrafish, rep2


title: HET, TSA treatment, zebrafish, rep1


title: DC1


title: RMB161


title: Balb/C treated with IL10 antibodies IL10_1

description: Balb/C treated with IL10 antibodies


title: WT, DMSO treatment, zebrafish, rep1


title: RMB165


title: RMB159


title: WT, DMSO treatment, zebrafish, rep4


title: M_NK_cell_4

first: Katsuyuki

last: Shiroguchi

department: Center for Biosystems Dynamics Research (BDR)

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: mm10
Supplementary files format and content: The detected copy number of RNA moelcules per tube (i.e., 200 cells) for each gene is listed.

growth_protocol: Freshly isolated

extract_protocol:
RNAs from cell lysate was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 200 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Two hundred cells were isolated from thymus or blood using FACS cell sorter

value: Blood lymphocyte

tag: cell subset


title: M_NK_cell_3


title: M_NK_cell_2


title: Balb/C treated with IL10 antibodies IL10_3

description: Balb/C treated with IL10 antibodies


title: Balb/C treated with DSS DSS_8

description: Balb/C treated with DSS

value: DSS


title: Balb/C treated with DSS DSS_5

description: Balb/C treated with DSS


title: M_CD8_sp_T_cell_1

value: Thymus T cell

value: TCRbeta+NK1.1-CD1d tet-CD4-CD8+


title: M_CD4_sp_T_cell_4

value: TCRbeta+NK1.1-CD1d tet-CD4+CD8-


title: Balb/C treated with DSS DSS_6

description: Balb/C treated with DSS


title: M_NK_cell_1


title: Balb/C treated with DNBS DNBS_14

description: Balb/C treated with DNBS

value: DNBS


title: RMB156

value: Adult


title: M_CD4_sp_T_cell_1


title: RMB153


title: M_CD8_sp_T_cell_3


title: M_CD8_sp_T_cell_4


title: Balb/C treated with DNBS DNBS_16

description: Balb/C treated with DNBS


title: M_CD8_sp_T_cell_2


title: M_CD4_sp_T_cell_2


title: Balb/C treated with DNBS DNBS_11

description: Balb/C treated with DNBS


title: M_CD4_minus_C2_iNKT_cell_3

value: Thymus iNKT cell

value: TCRbeta+NK1.1+CD1d tet+CD244+CXCR6+CD4-


title: RMB154


title: RMB157


title: RMB155


title: RMB158


title: RMB152


title: M_CD4_sp_T_cell_3


title: untreated Balb/C Control_4

description: untreated Balb/C


title: RMB151


title: M_CD4_minus_C2_iNKT_cell_2


title: M_CD4_minus_C2_iNKT_cell_1


title: M_CD4_plus_C2_iNKT_cell_4

value: TCRbeta+NK1.1+CD1d tet+CD244+CXCR6+CD4+


title: M_CD4_plus_C2_iNKT_cell_3


title: untreated Balb/C Control_1

description: untreated Balb/C

value: colon


title: M_CD4_plus_C2_iNKT_cell_1


title: M_CD4_minus_C2_iNKT_cell_4


title: M_CD4_plus_C2_iNKT_cell_2


title: RMB149


title: M_C0_iNKT_cell_4

value: TCRbeta+NK1.1+CD1d tet+CD244-CXCR6-