title: scTrioSeq2Met_CRC01_PT1_235

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_224

status: Public on Nov 29 2018

type: SRA

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

country: China

institute: Peking University

description: single cell DNA methylome seq

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The raw sequencing reads were trimmed to remove sequencing adapters, amplification primers, and low-quality bases in read ends.
For the data from scRNA-seq performed according to Tang protocol (Tang et al., 2009), trimmed clean reads were aligned to human reference genome (hg19) using STAR (v2.5.0) 2-pass mapping steps. For the data from scRNA-seq performed according to the multiplexed scRNA-seq method, the analyses were done as the previous paper (Dong et al., 2018).
For bisulfite sequencing data, trimmed clean reads were mapped to human reference genome (hg19) using Bismark (v0.7.6)
Genome_build: hg19
Supplementary_files_format_and_content: The FPKM.txt files include the FPKM values of RefSeq genes. The TPM.txt files include the TPM values of RefSeq genes. The SingleC files include the DNA methylation level of each singleC sites.

molecule: genomic DNA

organism: Homo sapiens

source_name: CRC

growth_protocol: The HEp-2 (ATCC CCL-23) cell line were cultured in RPMI 1640 with 10% FBS, and digested with trypsin before single cell picking.

extract_protocol:
The single viable cells were individually picked into 200-uL tubes containing lysis buffer. For scTrio-seq2, we used magnetic beads (Invitrogen, cat. #65011) to separate the nucleus and RNA of one single cell. We added 0.2 ?L magnetic beads to each single-cell lysis buffer. Then the single cells were lysed and vortexed for 1 min to release RNA. The lysis products were then centrifuged at 1,000 × g for 5 min at 4°C, and placed on the magnetic rack for 5 min. The magnetic beads can aggregate on the surface of the nucleus to maintain the nucleus in the pellet, while the RNA was released in the supernatants. The supernatants containing RNA were transferred to a new tube for transcriptome sequencing. The remaining beads containing a single nucleus were re-suspended with lysis buffer of scBS-seq for DNA methylation sequencing
For single-cell whole-genome bisulfite sequencing, the scBS-seq libraries were constructed according to the published protocol as described in 2017 (Clark et al., 2017). For CRC01 and CRC02, the transcriptome sequencing libraries were constructed according to Tang protocol (Tang et al., 2009); for the remaining patients, the transcriptome sequencing libraries were constructed according to a multiplexed scRNA-seq method, in which the poly T primers were combined with barcodes and unique molecule identifiers (UMIs) (Dong et al., 2018).

treatment_protocol: Informed consent was obtained from all patients preoperatively. Multi-regional sampling tissues were collected. For each tumor, 3-6 regions, including both surface and center areas, were sampled. Except for the MP of CRC01 which was sampled after six cycles of chemotherapy, other tumors were all sampled before treatment. Patient-derived tumors and adjacent normal tissue were collected and processed immediately after surgical resection. The dissected tissues were then mechanically dissociated and enzymatically digested to single-cell suspension using collagenase type II (Invitrogen, cat. #17101015) and collagenase type IV (Invitrogen, cat. #17104019). For 5 patients (CRC11, CRC12, CRC13, CRC14, and CRC15), leukocytes were depleted by magnetic-activated cell sorting (MACS) (CD45 Microbeads, Miltenyi Biotec, cat. #130-045-801) or fluorescence-activated cell sorting (FACS) (BV421 Mouse Anti-Human CD45, BD Horizon, cat. #563879).

tag: disease state

value: Carcinoma


title: scTrioSeq2Met_CRC01_PT1_231

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_237

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_229

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_284

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_230

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT2_320

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_221

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_218

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT2_318

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_226

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_297

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_216

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_215

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_213

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_212

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_211

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_210

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_206

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_204

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_209

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_203

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_201

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_202

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_236

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_238

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_PT1_228

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_529

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_527

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_509

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_517

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_122

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_123

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_115

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_112

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_521

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_110

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_116

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_111

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP5_109

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_507

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_196

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_NC_525

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_191

description: single cell DNA methylome seq


title: GES15-05048-745

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

data_processing:
All raw sequence files were processed using the Bismark software as follows:  For the kidney data from JAX laboratories, a Bismark-based pipeline was initially used as follows. All the samples were subjected to QC using the trim_galore module then trimming of the diversity adapters was performed by trimRRBSdiversityAdaptCustomers.py script from NuGen. High quality trimmed reads were aligned to all eight diversity outbred founder strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ,) separately using Bismark at default parameters. The alignment to founder genomes except C57BL/6J were converted to reference genome coordinates (mm10) using g2gtools v1 (https://github.com/churchill-lab/g2gtools). Then, we selected the reads which were mapped to the same locus in multiple founders strains (assigned to founder strains with minimum edit distance) or mapped uniquely to one founder strains by custom in-house script. The bed file of estimated methylation proportion of each founder (except C57BL/6J ) was converted to reference genome coordinate by g2gtools v1 and finally, combined to provide the  methylation proportion in each diversity outbred animals
Bismark output was reformated to the "CGmap" format for the next processing step to generate the CGfinal files.
CGfinal files: For each CpG site in each sample we estimated the methylation frequency as the number of methylated mapped read counts over the total mapped read counts.  Where available, the counts for the forward and reverse Cytosines of the CpG were pooled and treated as a single measurement.  We then computed a 95% confidence interval with a Bayesian approach using a Beta distribution (0.5,0.5) (“Jeffrey’s Prior”) for all methylation values
Genome_build: mm10
Supplementary_files_format_and_content:  [CGfinal files]  chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency

organism: Mus musculus

source_name: Kidney

extract_protocol: (JAX Laboratories Data) RRBS libraries were prepared using 100 ng DNA, the Ovation RRBS Methyl-Seq System 1–16 (NuGEN Technologies, San Carlo, CA) part number 0353, and the EpiTect Fast 96 Bisulfite Conversion kit (Qiagen, Hilden, Germany) part number 59720. The manufacturer’s protocols were followed except for the number of PCR cycles in the library amplification step, which was increased, from 12 to 13. Libraries were quantified using the Library Quantification Kit (Kapa Biosystems, Wilmington, MA) part number KK4835, normalized to 10nM, and pooled in groups of 12.  Each pool was sequenced 1 x 100 bp on one lane of the HiSeq2500 (Illumina, San Diego, CA) at The New York Genome Center (New York, NY).

tag: strain

value: Collaborative Cross strains, were developed by crossing eight unique and genetically diverseinbred mouse strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ

tag: tissue

value: Kidney

tag: age

tag: Sex

value: Female


title: scTrioSeq2Met_CRC01_MP4_185

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_188

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_192

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_184

description: single cell DNA methylome seq


title: GES15-05046-1056

value: Male


title: GES15-05047-1156


title: scTrioSeq2Met_CRC01_MP4_204

description: single cell DNA methylome seq


title: GES15-05044-1162


title: scTrioSeq2Met_CRC01_MP5_107

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_173

description: single cell DNA methylome seq


title: GES15-05045-1165


title: scTrioSeq2Met_CRC01_MP5_106

description: single cell DNA methylome seq


title: GES15-05042-996


title: GES15-05043-1000


title: scTrioSeq2Met_CRC01_MP4_203

description: single cell DNA methylome seq


title: GES15-05040-1306


title: GES15-05041-958


title: scTrioSeq2Met_CRC01_MP4_083

description: single cell DNA methylome seq


title: GES15-05039-1179


title: scTrioSeq2Met_CRC01_MP4_194

description: single cell DNA methylome seq


title: GES15-05038-1046


title: scTrioSeq2Met_CRC01_MP4_078

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_081

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_080

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_073

description: single cell DNA methylome seq


title: GES15-05037-1020


title: scTrioSeq2Met_CRC01_MP4_075

description: single cell DNA methylome seq


title: GES15-05036-1003


title: scTrioSeq2Met_CRC01_MP4_072

description: single cell DNA methylome seq


title: GES15-05034-953


title: scTrioSeq2Met_CRC01_MP4_183

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP4_066

description: single cell DNA methylome seq


title: GES15-05033-922


title: scTrioSeq2Met_CRC01_MP4_082

description: single cell DNA methylome seq


title: GES15-05032-1312


title: scTrioSeq2Met_CRC01_MP3_105

description: single cell DNA methylome seq


title: GES15-05031-1070


title: scTrioSeq2Met_CRC01_MP3_104

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP3_103

description: single cell DNA methylome seq


title: scTrioSeq2Met_CRC01_MP3_098

description: single cell DNA methylome seq


title: GES15-05028-957


title: GES15-05030-1029


title: GES15-05026-1290


title: Mouse_Muscle_SH060

data_processing:
All raw sequence files were processed using the BS_Seeker2 software in RRBS mode with standard parameters
Final processed files used in the analysis were modified from the BS_Seeker2 output files (".CGmap") to generate "CGfinal" files.
CGfinal files: For each CpG site in each sample we estimated the methylation frequency as the number of methylated mapped read counts over the total mapped read counts.  Where available, the counts for the forward and reverse Cytosines of the CpG were pooled and treated as a single measurement.  We then computed a 95% confidence interval with a Bayesian approach [64] using a Beta distribution (0.5,0.5) (“Jeffrey’s Prior”) for all methylation values [65]
Genome_build: mm10
Supplementary_files_format_and_content:  [CGfinal files]  chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency

source_name: Muscle

extract_protocol: (UCLA Data) For each sample 50-100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and dA-tailing was performed by the addition of Klenow Fragment 3’->5’ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP and d5mCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 2 µl of Illumina Ligation Mix 2 (Illumina, TruSeq Nano cat# FC-121-4001). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 300 bp. Bisulfite treatment was performed using Epitect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer's protocol, except that two consecutive rounds of conversion are performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30s; 12 cycles of 98°C for 15s, 60°C for 30s, 72°C for 30s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers. Libraries were sequenced 100 bp single-end on an Illumina HiSeq4000.

value: BALB/cByJ

value: Muscle


title: Mouse_Muscle_SH055


title: Mouse_Muscle_SH054


title: Mouse_Muscle_SH058


title: Mouse_Muscle_SH056


title: Mouse_Muscle_SH059


title: GES15-05024-1093


title: GES15-05023-1031


title: GES15-05021-1311


title: GES15-05020-1115


title: Mouse_Muscle_SH052


title: GES15-05029-981


title: Mouse_Muscle_SH057


title: GES15-05025-1077


title: Mouse_Muscle_SH050


title: GES15-05019-1103


title: GES15-05018-995


title: GES15-05027-696


title: GES15-05035-967


title: GES15-05017-992


title: Mouse_Muscle_SH048


title: GES15-05015-698


title: Mouse_Muscle_SH047


title: GES15-05016-956


title: Mouse_Muscle_SH053


title: Mouse_Muscle_SH046


title: GES15-05022-1010


title: GES15-05014-1268


title: GES15-05012-1200


title: Mouse_Muscle_SH051


title: Mouse_Muscle_SH043


title: GES15-05011-1199


title: GES15-05013-1237


title: Mouse_Muscle_SH045


title: GES15-05010-1041


title: GES15-05009-1157


title: Mouse_Muscle_SH041


title: Mouse_Muscle_SH040


title: Mouse_Muscle_SH037


title: Mouse_Muscle_SH038


title: Mouse_Muscle_SH049


title: GES15-05008-1149


title: GES15-05006-1007


title: GES15-05004-940


title: GES15-05007-1131


title: GES15-05005-952


title: Mouse_Muscle_SH035


title: GES15-05003-938


title: Mouse_Muscle_SH033


title: Mouse_Muscle_SH036


title: GES15-05002-777


title: Mouse_Muscle_SH044


title: Mouse_Muscle_SH032


title: scTrioSeq2Met_CRC01_MP5_113

description: single cell DNA methylome seq


title: Mouse_Muscle_SH042


title: GES15-05001-776


title: GES15-04999-701


title: GES15-05000-763


title: Mouse_Muscle_SH029


title: Mouse_Muscle_SH039


title: Mouse_Muscle_SH030


title: Mouse_Muscle_SH028


title: Mouse_Muscle_SH031


title: GES15-04998-1285


title: Mouse_Muscle_SH027


title: GES15-04997-1181


title: GES15-04996-982


title: GES15-04994-959


title: GES15-04995-960


title: Mouse_Muscle_SH025


title: Mouse_Muscle_SH023


title: Mouse_Muscle_SH026


title: Mouse_Muscle_SH024


title: Mouse_Muscle_SH034


title: GES15-04992-723


title: GES15-04993-828


title: GES15-04991-661


title: Mouse_Muscle_SH022


title: Mouse_Muscle_SH021


title: GES15-04990-1252


title: GES15-04988-1196


title: Mouse_Muscle_SH020


title: Mouse_Muscle_SH019


title: GES15-04989-1218


title: Mouse_Muscle_SH018


title: GES15-04986-1153


title: Mouse_Muscle_SH017


title: GES15-04987-1193


title: Mouse_Muscle_SH015


title: Mouse_Muscle_SH016


title: Mouse_Muscle_SH014


title: GES15-04983-1042


title: GES15-04982-804


title: GES15-04984-1076


title: GES15-04985-1138


title: Mouse_Muscle_SH013


title: Mouse_Muscle_SH012


title: Mouse_Muscle_SH010


title: Mouse_Muscle_SH011


title: GES15-04981-1159


title: Mouse_Muscle_SH009


title: GES15-04979-1057


title: GES15-04980-1135


title: Mouse_Muscle_SH007


title: Mouse_Muscle_SH008


title: GES15-04974-781


title: GES15-04973-767


title: Mouse_Muscle_SH004


title: GES15-04975-795


title: Mouse_Muscle_SH005


title: GES15-04976-929


title: GES15-04977-969


title: GES15-04978-972


title: Mouse_Muscle_SH006


title: Mouse_Muscle_SH002


title: Mouse_Muscle_SH003


title: GES15-04972-765


title: GES15-04969-1213


title: GES15-04970-1215


title: GES15-04967-1114


title: GES15-04971-1279


title: GES15-04968-1163


title: GES15-04965-989


title: GES15-04966-1023


title: GES15-04964-907


title: GES15-04962-760


title: GES15-04963-823


title: GES15-04961-756


title: Mouse_Lung_SH057

source_name: Lung

value: Lung


title: Mouse_Lung_SH059


title: Mouse_Lung_SH056


title: Mouse_Lung_SH060


title: Mouse_Lung_SH058


title: Mouse_Muscle_SH001


title: GES15-04956-1318


title: GES15-04959-719


title: GES15-04957-677


title: GES15-04960-746


title: GES15-04958-704


title: GES15-04953-1247


title: GES15-04954-1265


title: GES15-04955-1309


title: GES15-04950-1224


title: GES15-04952-1242


title: Mouse_Lung_SH054


title: Mouse_Lung_SH049


title: Mouse_Lung_SH046


title: Mouse_Lung_SH052


title: Mouse_Lung_SH039


title: Mouse_Lung_SH047


title: GES15-04949-1201


title: Mouse_Lung_SH050


title: Mouse_Lung_SH045


title: Mouse_Lung_SH042


title: Mouse_Lung_SH053


title: Mouse_Lung_SH055


title: GES15-04947-1191


title: Mouse_Lung_SH048


title: Mouse_Lung_SH051


title: Mouse_Lung_SH037


title: Mouse_Lung_SH036


title: GES15-04948-1197


title: Mouse_Lung_SH038


title: Mouse_Lung_SH035


title: Mouse_Lung_SH040


title: Mouse_Lung_SH034


title: Mouse_Lung_SH033


title: Mouse_Lung_SH032


title: GES15-04943-1100


title: GES15-04945-1172


title: GES15-04946-1174


title: GES15-04944-1118


title: Mouse_Lung_SH031


title: GES15-04942-1078


title: GES15-04941-803


title: GES15-04940-788


title: Mouse_Lung_SH030


title: Mouse_Lung_SH029


title: Mouse_Lung_SH023


title: Mouse_Lung_SH025


title: Mouse_Lung_SH022


title: Mouse_Lung_SH027


title: Mouse_Lung_SH026


title: Mouse_Lung_SH024


title: GES15-04935-709


title: GES15-04933-692


title: GES15-04937-937


title: GES15-04934-693


title: GES15-04938-941


title: GES15-04936-936


title: Mouse_Lung_SH021


title: Mouse_Lung_SH028


title: GES15-04939-1058


title: Mouse_Lung_SH020


title: Mouse_Lung_SH019


title: GES15-04932-685


title: GES15-04931-711


title: Mouse_Lung_SH018


title: Mouse_Lung_SH017


title: GES15-04928-1250


title: GES15-04930-682


title: GES15-04929-1307


title: Mouse_Lung_SH016


title: Mouse_Lung_SH015


title: GES15-04927-1140


title: Mouse_Lung_SH014


title: GES15-04926-1121


title: GES15-04923-1107


title: GES15-04922-1006


title: GES15-04925-1098


title: GES15-04924-789


title: GES15-04919-710


title: Mouse_Lung_SH009


title: Mouse_Lung_SH013


title: Mouse_Lung_SH011


title: Mouse_Lung_SH010


title: Mouse_Lung_SH008


title: GES15-04918-1210


title: GES15-04920-779


title: Mouse_Lung_SH007


title: Mouse_Lung_SH012


title: GES15-04916-670


title: Mouse_Lung_SH006


title: Mouse_Lung_SH004


title: GES15-04915-1099


title: GES15-04914-1097


title: GES15-04921-816


title: GES15-04913-831


title: Mouse_Lung_SH003


title: Mouse_Liver_SH060

source_name: Liver

value: Liver


title: GES15-04912-801


title: GES15-04909-735


title: GES15-04911-787


title: GES15-04908-676


title: GES15-03361-DO-0836


title: Mouse_Liver_SH057


title: Mouse_Liver_SH055


title: Mouse_Liver_SH054


title: Mouse_Liver_SH056


title: Mouse_Liver_SH058


title: GES15-03360-DO-1300


title: Mouse_Liver_SH053


title: Mouse_Lung_SH005


title: Mouse_Lung_SH001


title: GES15-03359-DO-1195


title: Mouse_Liver_SH051


title: Mouse_Lung_SH002


title: GES15-03358-DO-1035


title: GES15-03357-DO-1033


title: Mouse_Liver_SH052


title: GES15-03356-DO-0950


title: GES15-04910-683


title: Mouse_Liver_SH059


title: Mouse_Liver_SH049


title: GES15-03355-DO-1182


title: GES15-04907-1061


title: GES15-03354-DO-1025


title: Mouse_Liver_SH048


title: GES15-04906-790


title: Mouse_Liver_SH047


title: GES15-03352-DO-1316


title: GES15-03353-DO-0951


title: Mouse_Liver_SH046


title: GES15-03351-DO-1267


title: GES15-03349-DO-1015


title: Mouse_Liver_SH045


title: Mouse_Liver_SH043


title: Mouse_Liver_SH050


title: Mouse_Liver_SH042


title: GES15-03348-DO-0669


title: GES15-03347-DO-0909


title: Mouse_Liver_SH040


title: Mouse_Liver_SH041


title: GES15-03346-DO-1299


title: GES15-03344-DO-1148


title: GES15-03342-DO-0819


title: GES15-03341-DO-0818


title: Mouse_Liver_SH034


title: Mouse_Liver_SH035


title: Mouse_Liver_SH036


title: Mouse_Liver_SH037


title: GES15-03350-DO-1263


title: Mouse_Liver_SH033


title: Mouse_Liver_SH032


title: GES15-03340-DO-0911


title: GES15-03343-DO-0979


title: GES15-03337-DO-0980


title: GES15-03338-DO-1160


title: Mouse_Liver_SH044


title: Mouse_Liver_SH031


title: GES15-03345-DO-1037


title: GES15-03335-DO-0766


title: GES15-03334-DO-0673


title: Mouse_Liver_SH038


title: Mouse_Liver_SH029


title: Mouse_Liver_SH039


title: Mouse_Liver_SH028


title: GES15-03333-DO-0945


title: Mouse_Liver_SH027


title: Mouse_Liver_SH026


title: Mouse_Liver_SH025


title: GES15-03332-DO-0923


title: GES15-03339-DO-1124


title: GES15-03330-DO-0721


title: GES15-03329-DO-0686


title: GES15-03327-DO-1251


title: Mouse_Liver_SH024


title: Mouse_Liver_SH023


title: Mouse_Liver_SH030


title: Mouse_Liver_SH020


title: GES15-03328-DO-0674


title: Mouse_Liver_SH022


title: Mouse_Liver_SH019


title: Mouse_Liver_SH018


title: Mouse_Liver_SH021


title: GES15-03336-DO-0817


title: GES15-03325-DO-1243


title: GES15-03324-DO-1222


title: GES15-03323-DO-0712


title: GES15-03322-DO-1067


title: GES15-03321-DO-1208


title: Mouse_Liver_SH015


title: Mouse_Liver_SH017


title: Mouse_Liver_SH016


title: Mouse_Liver_SH014


title: Mouse_Liver_SH013


title: GES15-03331-DO-1209


title: GES15-03320-DO-1297


title: Mouse_Liver_SH012


title: GES15-03317-DO-0744


title: GES15-03318-DO-1119


title: Mouse_Liver_SH011


title: GES15-03326-DO-1249


title: GES15-03315-DO-1248


title: Mouse_Liver_SH010


title: Mouse_Liver_SH009


title: GES15-03314-DO-0809


title: Mouse_Liver_SH007


title: Mouse_Liver_SH008


title: Mouse_Liver_SH006


title: Mouse_Liver_SH004


title: Mouse_Liver_SH005


title: mOSN_3EnhKO_RNAseq_rep1

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

library_source: transcriptomic

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

molecule: total RNA

source_name: mature olfactory sensory neurons

extract_protocol:
Crosslinked-ChIP: Chromatin from formaldehyde cross-linked cells was sheared on a Covaris S220 Focused-ultrasonicator to a size range of 200-500bp. Approximately 1-2ug of sheared chromatin was used for immunoprecipitation with antibodies, and precipitated DNA was column purified. RNA: Cells were lysed in Trizol-LS (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
Crosslinked-ChIP: ChIP-seq Libraries were prepared using a Nugen Ultralow V2 kit. RNA: RNA-seq libraries were prepared using a TruSeq Stranded Total RNA with Ribo-Zero Gold Set B kit (Illumina RS-1222302).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical), 4mM MgCl2, and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 5 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting. For Krt5Cre knockout cells, at 6-weeks of age, deletion of the conditional allele in horizontal basal cells was induced by two intraperitoneal injections of tamoxifen twenty-four hours apart. One week later, differentiation of horizontal basal cells into olfactory cell types was induced by intraperitoneal injection with methimazole, which triggers ablation of olfactory epithelium and regeneration of the tissue from horizontal basal cells. The olfactory epithelium was allowed to regenerate for 8-weeks, and then  TdTomato+ cell were purified by FACS. TdTomato bright and dim populations were collected separately, followed by RNA-seq.

tag: genotype/variation

value: OMP-IRES-GFP; H-/-; Lipsi-/-; Sfaktiria-/-

tag: tissue/cell type

value: mature olfactory sensory neurons


title: Mouse_Liver_SH001


title: Mouse_Liver_SH003


title: Mouse_Liver_SH002


title: GES15-03319-DO-0821


title: Mouse_Kidney_SH056


title: mOSN_3EnhKO_RNAseq_rep2


title: Krt5Cre_Lhx2KO_Bright_RNAseq_rep1

source_name: TdTomato dim cells from the olfactory epithelium

value: Krt5Cre; Lhx2fl/fl;Rosa-CAG-tdtom+/fl


title: Krt5Cre_Lhx2Het_Dim_RNAseq_rep1

source_name: TdTomato bright cells from the olfactory epithelium

value: Krt5Cre; Lhx2+/fl;Rosa-CAG-tdtom+/fl


title: Krt5Cre_Lhx2KO_Dim_RNAseq_rep1

value: TdTomato dim cells from the olfactory epithelium


title: Krt5Cre_Lhx2Het_Bright_RNAseq_rep1

value: TdTomato bright cells from the olfactory epithelium


title: GES15-03316-DO-0758


title: Mouse_Kidney_SH053


title: Mouse_Kidney_SH054


title: Mouse_Kidney_SH051


title: Mouse_Kidney_SH050


title: Mouse_Kidney_SH049


title: ISC1

first: Pingping

last: Zhu

address: Datun Road 15#

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters
Following reads quality control: Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length
Then reads quality was inspected using the FastQC software then output statistical result
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: intestine

extract_protocol:
Lgr5GFP mice were obtained in SPF condition, and ISCs&non-ISCs were isolated through FACS. Total RNA was isolated from cells/tissues using the Trizol (invitrogen) according to the manufacturer’s protocol. RNA purity was assessed by ND-1000 Nanodrop required A260/280≥1.8, A260/A230≥2.0. RNA integrity (RIN) was evaluated by Agilent 2200 TapeStation (Agilent Technologies, USA) requiring RIN≥7.0. Briefly, rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) , then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp.
The purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then sequenced on HiSeq 3000 with 2 X 150 bp mode

tag: cell type

value: Lgr5+ ISC

value: intestine

value: 2 month


title: non-ISC1

value: Lgr5- non-ISC


title: Mouse_Kidney_SH048

value: Kidney


title: Mouse_Kidney_SH047


title: Mouse_Kidney_SH046


title: Mouse_Kidney_SH055

value: Female


title: Mouse_Kidney_SH045


title: Mouse_Kidney_SH044


title: Mouse_Kidney_SH042


title: Mouse_Kidney_SH041


title: Mouse_Kidney_SH040

value: Male


title: Mouse_Kidney_SH039

value: BALB/cByJ


title: Mouse_Kidney_SH037


title: Mouse_Kidney_SH038


title: total RNA from melanocyte [3]

type: RNA

city: Kobe

first: Susumu

last: Fujiwara

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: dermatology

country: Japan

institute: Kobe univ

description:
normal melanocyte sample
SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpringGX version12.5

label: biotin

source_name: melanocyte

label_protocol: TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®

extract_protocol: total RNA was extracted and purified using Qiagen AllPrep DNA/RNA Micro Kit according to standard instructions

tag: gender

value: female

tag: source lesion

value: abdominal skin

value: melanocyte

value: normal


title: Mouse_Kidney_SH036


title: total RNA from melanocyte [6]

description:
commercially available melanocyte adult
SAMPLE 6

value: unknown


title: total RNA from melanoma [9]

description:
cell line melanoma
SAMPLE 9

source_name: melanoma

value: male

tag: cell line

value: cell line G361

value: melanoma

value: malignant


title: total RNA from melanoma [10]

description:
cell line melanoma
SAMPLE 10

value: cell line HM3KO


title: 21_HIV-1JR-CSF 100TCID50

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description:
21_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: HIV-1JR-CSF 100TCID50

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: EpiVaginal Tissues were in received in sterile conditions and equilibrated at 37˚C, 5% CO2 for 24 h.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc).

treatment_protocol: The culture inserts containing tissues were transferred into new 12 well plates with peripheral blood mononuclear cells (PBMCs) in the basal chamber. Tissues were apically treated with rhSP-D or HIV-1 or both or left untreated for 24 h. After incubation, tissues were collected in trizol and further processed for Microarray analysis.

value: EpiVaginal Tissues


title: 14_rhSP-D (100μg/ml) + HIV-1JR-CSF

description:
14_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)

source_name: rhSP-D (100μg/ml) + HIV-1JR-CSF


title: Mouse_Kidney_SH043


title: total RNA from melanoma [8]

description:
cell line melanoma
SAMPLE 8

value: cell line SK-mel-28


title: Mouse_Kidney_SH035


title: total RNA from melanocyte [7]

description:
commercially available melanocyte adult
SAMPLE 7


title: 1_rhSP-D (100μg/ml)

description:
1_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)

source_name: rhSP-D (100μg/ml)


title: total RNA from melanocyte [5]

description:
commercially available melanocyte new born
SAMPLE 5


title: 20_HIV-1JR-CSF 100TCID50

description:
20_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)


title: 8_untreated

description:
8_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)

source_name: untreated


title: total RNA from melanocyte [1]

description:
normal melanocyte sample
SAMPLE 1

value: cheek


title: total RNA from melanoma [2]

description:
NM melanoma sample
SAMPLE 2


title: total RNA from melanoma [4]

description:
ALM melanoma sample
SAMPLE 4

value: sole


title: 15_rhSP-D (100μg/ml) + HIV-1JR-CSF

description:
15_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)


title: 2_rhSP-D (100μg/ml)

description:
2_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)


title: 9_untreated

description:
9_Dr_Taruna
EpiVagina; Tissues (MatTek Corporation)


title: Mouse_Kidney_SH033

value: Kidney

value: Female


title: Mouse_Kidney_SH034

value: BALB/cByJ


title: Mouse_Kidney_SH032


title: Mouse_Kidney_SH031


title: Mouse_Kidney_SH030

value: Male


title: Mouse_Kidney_SH029


title: Mouse_Kidney_SH027


title: Mouse_Kidney_SH026


title: R46_NA_N_30min_h3k27ac

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Base calls were performed using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).
Reads were aligned to Amel_4.5 (OGS v. 3.2 annotation set) using Bowtie2 v. 2.1.0 with default settings
Mapped sequence data were analyzed using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7. Samples were converted into Tag Directories, and QC was performed using read mapping and GC bias statistics.
Genome_build: Amel_4.5 (OGS v. 3.2 annotation)
Supplementary_files_format_and_content: BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings.  Individual technical replicate IP samples were combined into pooled bigWig files.

organism: Apis mellifera

source_name: pooled whole brain (10 bees)

growth_protocol: Honey bee (Apis mellifera) workers were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL, from June to August 2014. For the RNA-Seq experiment, we used three colonies, each headed by a queen that was instrumentally inseminated with semen from a single (different) drone (Single Drone Inseminated colony, “SDI”); because of hapolodiploidy, the resulting female worker offspring were highly related to each other (average coefficient of relatedness, r = 0.75), thus decreasing within-trial genetic variation. One-day-old adult bees were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent degradation during dissection. The cuticle of the head capsule was removed and each head was placed in PBS + Protease Inhibitor Cocktail (Roche) at -20ºC for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed.  The brains were placed in a new 1.5ml tube and kept frozen (-80°C) until ChIP. ChIP was performed with a Diagenode iDeal ChIP kit and the standard protocol using Abcam ab4729 (rb polyclonal anti-H3K27Ac) antibodies. 1/10 volume input  DNA samples were collected from each aliquot and pooled and used as a background control for peak calling
ChIP-Seq libraries were constructed with KAPA LTP library kits (KK8230) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qubit (invitrogen). Single-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Groups were created by dividing emerged bees into groups of ten, individually marking on their thoraces with a spot of paint (Testor’s PLA), and keeping them in clear plastic Petri dishes (100 x 20 mm). The dishes were supplied with one 2 ml tube of 30% sucrose solution and one small piece of honeycomb containing honey (containing about 6 cells). Groups were held in the incubator for 7 days prior to the beginning of the experiment. We used a recently developed assay shown to induce natural queen rearing behavior in the laboratory (Shpigler and Robinson, 2015). Briefly, 7-day-old bees were exposed to a 4-day-old queen larva located in a waxen queen cell for 5 min. The experiment was conducted in an incubator room set to mimic the normal in-hive conditions when brood care behavior is performed (34°±0.5 C, 50% ± 10% RH). Detailed observations were performed for 5 min after the queen larva was introduced to the dish, during which the bees enter the queen cell to interact with the larva. We focused on two behaviors: cell inspection, which consists of short interactions (< 10 sec) and nursing, which consists of longer interactions (11-90 sec), marked by the characteristics of feeding endogenously produced royal jelly and abdominal contractions. For each bee, we recorded the number of visits into the queen cell, the length of each visit, and the total amount of time spent in the cell out of the five-minute assay.These bees were frozen immediately in liquid nitrogen and individually placed in a 1.5 mL tube stored in a –80°C freezer for further analysis. For transcriptomic profiling, experimental bees and matched control bees were used for each time point, summing to a total of 60 bees per colony. The experiment was repeated with three different colonies, summing to a total sample size of 176 bees.

tag: nurturance

value: N

tag: time

tag: colony

value: whole brain

tag: chip antibody

value: Abcam ab4729 (rabbit polyclonal anti-H3K27Ac, lot# GR150367-2)


title: Con-rep1

city: Dresden

first: Luis

middle: Fernando

last: Delgadillo Silva

address: Fetscherstraße 105

country: Germany

institute: CRTD

data_processing:
Illumina NextSeq Control/RTA2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to zebrafish genome GRCz10, using GSNAP from Ensembl gene annotation, version 87
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Danio rerio

source_name: Pancreatic beta-cells

extract_protocol:
Beta-cell isolated from islets were sorted and analyzed using FACS-Aria II (BD Bioscience). For dissociation, islets were collected in PBS chilled on ice. After one washing with ice cold PBS, islets were dissociated into single cells by incubation in TrypLE (ThermoFisher, 12563029) with 0.1% Pluronic F-68 (ThermoFisher, 24040032) at 37˚C in a benchtop shaker set at 350 rpm for 50 min. Following dissociation, TrypLE was inactivated with 10% FBS, and the cells pelleted by centrifugation at 500 g for 10 min at 4˚C. The supernatant was carefully discarded and the pellet re-suspended in 500 ml of HBSS (without Ca2+, Mg2+)+0.1% Pluronic F-68. To remove debris, the solution was passed over a 30 mm cell filter (Miltenyi Biotec, 130-041-407).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic beta-cells

value: 3 months old

tag: genotype

value: wild type


title: Mouse_Kidney_SH025


title: R41_NA_N_120min_h3k27ac


title: R46_NA_N_120min_h3k27ac


title: R46_NA_K_120min_h3k27ac

value: K


title: R41_NA_N_30min_h3k27ac


title: Mouse_Kidney_SH024


title: Con-rep2


title: R46_NA_K_30min_h3k27ac


title: R41_NA_K_120min_h3k27ac


title: R41_NA_K_30min_h3k27ac


title: Mouse_Kidney_SH022


title: Mouse_Kidney_SH021


title: Mouse_Kidney_SH023


title: N257_120min_cR41

data_processing:
Base calls were performed using CASAVA v. 1.8.2
Reads were aligned to Amel_4.5 (OGS v. 3.2 annotation set) using TopHat2 v. 2.0.10 with Bowtie2 v. 2.1.0 and Samtools v. 0.1.18
Deformed Wing Virus (DWV) alignments were calculated by aligning to the Pennsylvania variant of the DWV genome (GenBank accession: AY292384) using Bowtie 2 v. 2.1.0, and filtering took place during downstream bioinformatic analysis
Tags were counted using htseq-count in HTSeq v. 0.6.1
Genome_build: Amel_4.5 (OGS v. 3.2 annotation) with Pennsylvania build of DWV (GenBank accession: AY292384)
Supplementary_files_format_and_content: tab-delimited tag counts were generated using htseq-count.

source_name: mushroom body

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent RNA degradation during dissection. The cuticle of the head capsule was removed and each head was placed in RNAlaterICE (Life Technologies) at -20°C for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed. Using a fine scalpel, the optic lobes were removed and a horizontal incision was made across the midbrain through the posterior protocerebral lobe. The lower part of the midbrain containing the antennal lobes and the subesophageal ganglion were removed. The upper part of the midbrain containing mostly the mushroom bodies (MB) and the central brain was used for gene expression analysis. The MBs were placed in a new 1.5 mL tube and kept frozen (-80°C) until RNA extraction. RNA extraction was performed with a PicoPure RNA Isolation Kit (Applied Biosystems; Lot #: 1210063) and the standard protocol, including DNase treatment (QIAGEN) to remove genomic DNA contamination. 550 ng RNA from each sample (except for 19 samples that yielded 350- 550 ng) were used for whole mRNA expression analysis.
RNA-seq libraries were constructed with the TruSeq® Stranded mRNA HT (high throughput kit, Illumina cat #: RS-122-2103) using an ePMotion 5075 robot (Eppendorf) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qPCR. Single-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

value: mushroom body

tag: index

value: CTGAAGCT-CAGGACGT

tag: lane


title: Mouse_Kidney_SH019

source_name: Kidney

tag: strain


title: Mouse_Kidney_SH020

tag: tissue


title: Mouse_Kidney_SH018

tag: age


title: N249_120min_cR41

value: CTGAAGCT-GGCTCTGA


title: N243_120min_cR41

value: CTGAAGCT-TATAGCCT


title: N248_120min_cR41

value: CTGAAGCT-CCTATCCT


title: N242_120min_cR41

value: ATTCAGAA-GTACTGAC


title: N254_120min_cR41

value: CTGAAGCT-AGGCGAAG


title: N255_120min_cR41

value: CTGAAGCT-TAATCTTA


title: ISC_circPan3-/-

description: This is circPan3 KO ISCs

hyb_protocol: hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000 and analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

data_processing: All resulting .CEL files for each array type were processed as a single group via the Affymetrix Power Tools (APT) package using sketch normalization and the RMA algorithm to summarize probeset signal.

source_name: circPan3-/- Lgr5GFP+ ISCs

label_protocol: 10 mg of cRNA was carried into the second cycle, first strand cDNA synthesis reaction. 5.5 mg of single-stranded cDNA was fragmented and biotin-labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol:
2´105 ISCs were isolated from circPan3+/+;Lgr5GFP-CreERT2 or circPan3-/-;Lgr5GFP-CreERT2 mice. For FACS enrichment, 8 week-old mice were anesthetized and small intestine cells were collected, followed by ISCs sorting through a BD AriaIII sorter.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: small intestine

value: intestinal stem cells


title: N244_120min_cR41

value: N

value: CTGAAGCT-ATAGAGGC


title: N256_120min_cR41

value: CTGAAGCT-GTACTGAC


title: Mouse_Kidney_SH017

value: BALB/cByJ

value: Kidney

tag: Sex

value: Male


title: ISC_circPan3+/+

description: This is circPan3 WT ISCs

source_name: circPan3+/+ Lgr5GFP+ ISCs


title: N233_120min_cR02

value: ATTACTCG-CCTATCCT


title: N234_120min_cR02

value: mushroom body

value: ATTACTCG-GGCTCTGA


title: N232_120min_cR02

value: ATTACTCG-ATAGAGGC


title: Mouse_Kidney_SH016


title: Mouse_Kidney_SH015

value: Female


title: N231_120min_cR02

value: ATTACTCG-TATAGCCT


title: Mouse_Kidney_SH013


title: N228_120min_cR02

value: TCTCGCGC-GTACTGAC


title: N227_120min_cR02

value: TCTCGCGC-CAGGACGT


title: Mouse_Kidney_SH014


title: N219_120min_cR40

value: CTGAAGCT-TAATCTTA


title: N221_120min_cR02

value: TCTCGCGC-CCTATCCT


title: N223_120min_cR02

value: TCTCGCGC-AGGCGAAG


title: N222_120min_cR02

value: N

value: TCTCGCGC-GGCTCTGA


title: Mouse_Kidney_SH012


title: N226_120min_cR02

value: TCTCGCGC-TAATCTTA


title: N216_120min_cR40

value: CTGAAGCT-AGGCGAAG


title: Mouse_Kidney_SH011

value: BALB/cByJ

value: Kidney


title: Mouse_Kidney_SH010

value: Male


title: Mouse_Kidney_SH009


title: N215_120min_cR40

value: mushroom body

value: CTGAAGCT-GGCTCTGA


title: N214_120min_cR40

value: CTGAAGCT-CCTATCCT


title: N212_120min_cR40

value: CTGAAGCT-ATAGAGGC


title: N208_120min_cR40

value: ATTCAGAA-TAATCTTA


title: N210_120min_cR40

value: ATTCAGAA-GTACTGAC


title: N211_120min_cR40

value: CTGAAGCT-TATAGCCT


title: N209_120min_cR40

value: ATTCAGAA-CAGGACGT


title: Mouse_Kidney_SH008


title: N202_120min_cR40

value: ATTCAGAA-AGGCGAAG


title: N158_60min_cR41


title: Mouse_Kidney_SH007


title: Mouse_Kidney_SH006


title: N154_60min_cR41

value: ATTCAGAA-GGCTCTGA


title: N153_60min_cR41

value: N

value: ATTCAGAA-CCTATCCT


title: Mouse_Kidney_SH005

value: Female


title: N150_60min_cR41

value: CGCTCATT-GTACTGAC


title: N151_60min_cR41

value: ATTCAGAA-TATAGCCT


title: N147_60min_cR41

value: CGCTCATT-CAGGACGT


title: N152_60min_cR41

value: ATTCAGAA-ATAGAGGC


title: Mouse_Kidney_SH003

value: Kidney


title: N141_60min_cR41

value: mushroom body

value: CGCTCATT-TAATCTTA


title: N134_60min_cR02

value: TCTCGCGC-TATAGCCT


title: Mouse_Kidney_SH004


title: N148_60min_cR41

value: ATTCAGAA-TAATCTTA


title: N138_60min_cR02

value: TCTCGCGC-ATAGAGGC


title: Mouse_Kidney_SH002


title: N133_60min_cR02

value: TCTCGCGC-GTACTGAC


title: N132_60min_cR02

value: TCTCGCGC-CAGGACGT


title: Mouse_Kidney_SH001


title: Mouse_Blood_SH100

source_name: Blood

value: Blood

value: Male


title: N131_60min_cR02

value: N

value: TCTCGCGC-TAATCTTA


title: N125_60min_cR02

value: TCTCGCGC-GGCTCTGA


title: N127_60min_cR02

value: TCTCGCGC-AGGCGAAG


title: N124_60min_cR02

value: TCTCGCGC-CCTATCCT


title: N155_60min_cR41

value: ATTCAGAA-AGGCGAAG


title: N123_60min_cR02


title: N121_60min_cR02


title: Mouse_Blood_SH099


title: Mouse_Blood_SH097


title: N119_60min_cR40

value: ATTCAGAA-GGCTCTGA


title: N116_60min_cR40

value: ATTCAGAA-CCTATCCT


title: N115_60min_cR40

value: mushroom body

value: ATTCAGAA-ATAGAGGC


title: N114_60min_cR40

value: ATTCAGAA-TATAGCCT


title: Mouse_Blood_SH095

value: Female


title: Mouse_Blood_SH096


title: N112_60min_cR40

value: CGCTCATT-CAGGACGT


title: N113_60min_cR40

value: CGCTCATT-GTACTGAC


title: N111_60min_cR40

value: CGCTCATT-TAATCTTA


title: N110_60min_cR40

value: CGCTCATT-AGGCGAAG


title: Mouse_Blood_SH094

value: Blood


title: N109_60min_cR40

value: N

value: CGCTCATT-GGCTCTGA


title: Mouse_Blood_SH093


title: Mouse_Blood_SH092


title: N103_60min_cR40

value: CGCTCATT-CCTATCCT


title: N059_30min_cR41


title: N058_30min_cR41


title: Mouse_Blood_SH098

value: Male


title: N053_30min_cR41

value: ATTACTCG-GTACTGAC


title: Mouse_Blood_SH091


title: N054_30min_cR41

value: CGCTCATT-TATAGCCT


title: N056_30min_cR41

value: CGCTCATT-ATAGAGGC


title: N050_30min_cR41

value: ATTACTCG-CAGGACGT


title: N057_30min_cR41

value: mushroom body


title: Mouse_Blood_SH090


title: N043_30min_cR41

value: ATTACTCG-AGGCGAAG


title: N046_30min_cR41

value: ATTACTCG-TAATCTTA


title: Mouse_Blood_SH089


title: N039_30min_cR02

value: CGGCTATG-TAATCTTA


title: Mouse_Blood_SH088


title: N037_30min_cR02

value: CGGCTATG-GGCTCTGA


title: N036_30min_cR02

value: CGGCTATG-GTACTGAC


title: N035_30min_cR02

value: CGGCTATG-CCTATCCT


title: Mouse_Blood_SH086


title: Mouse_Blood_SH087


title: N033_30min_cR02

value: CGGCTATG-TATAGCCT


title: Mouse_Blood_SH085

value: Blood

value: Female


title: Mouse_Blood_SH084


title: N023_30min_cR02

value: N

value: CTGAAGCT-GTACTGAC


title: Mouse_Blood_SH081


title: N034_30min_cR02

value: CGGCTATG-ATAGAGGC


title: Mouse_Blood_SH082


title: N017_30min_cR40

value: ATTACTCG-GTACTGAC


title: N013_30min_cR40


title: N012_30min_cR40


title: Mouse_Blood_SH080

value: Male


title: N011_30min_cR40

value: ATTACTCG-GGCTCTGA


title: N010_30min_cR40

value: ATTACTCG-CCTATCCT


title: Mouse_Blood_SH079


title: N009_30min_cR40

value: mushroom body

value: ATTACTCG-ATAGAGGC


title: N019_30min_cR40

value: CGCTCATT-ATAGAGGC


title: K257_120min_cR41

value: K

value: TAATGCGC-CAGGACGT


title: N008_30min_cR40

value: ATTACTCG-TATAGCCT


title: N030_30min_cR02

value: CGGCTATG-CAGGACGT


title: K255B_120min_cR41

value: TAATGCGC-TAATCTTA


title: Mouse_Blood_SH078

value: Blood


title: K252_120min_cR41

value: TAATGCGC-GGCTCTGA


title: N018_30min_cR40

value: N

value: CGCTCATT-TATAGCCT


title: K248_120min_cR41

value: TAATGCGC-CCTATCCT


title: N021_30min_cR02

value: CTGAAGCT-CAGGACGT


title: N038_30min_cR02

value: CGGCTATG-AGGCGAAG


title: Mouse_Blood_SH083

value: Female


title: Mouse_Blood_SH077

value: Male


title: K254B_120min_cR41

value: mushroom body

value: TAATGCGC-AGGCGAAG


title: K244_120min_cR41

value: TAATGCGC-ATAGAGGC


title: Mouse_Blood_SH076


title: N014_30min_cR40

value: ATTACTCG-CAGGACGT


title: Mouse_Blood_SH074


title: K233_120min_cR02

value: K

value: TCCGGAGA-CCTATCCT


title: K242_120min_cR41

value: GAATTCGT-GTACTGAC


title: K231_120min_cR02

value: TCCGGAGA-TATAGCCT


title: K243_120min_cR41

value: TAATGCGC-TATAGCCT


title: K234_120min_cR02

value: TCCGGAGA-GGCTCTGA


title: K256_120min_cR41

value: TAATGCGC-GTACTGAC


title: K228_120min_cR02

value: AGCGATAG-GTACTGAC


title: K227_120min_cR02

value: AGCGATAG-CAGGACGT


title: K222_120min_cR02

value: AGCGATAG-GGCTCTGA


title: K226_120min_cR02

value: AGCGATAG-TAATCTTA


title: K223_120min_cR02

value: AGCGATAG-AGGCGAAG


title: K221_120min_cR02

value: AGCGATAG-CCTATCCT


title: Mouse_Blood_SH071

value: Blood

value: Female


title: Mouse_Blood_SH066

value: Male


title: Mouse_Blood_SH068


title: K219_120min_cR40

value: mushroom body

value: TAATGCGC-TAATCTTA


title: Mouse_Blood_SH069


title: Mouse_Blood_SH072


title: K211B_120min_cR40

value: K


title: K216_120min_cR40

value: TAATGCGC-AGGCGAAG


title: Mouse_Blood_SH070


title: K212_120min_cR40

value: TAATGCGC-ATAGAGGC


title: K209_120min_cR40

value: GAATTCGT-CAGGACGT


title: Mouse_Blood_SH075


title: K232_120min_cR02

value: TCCGGAGA-ATAGAGGC


title: Mouse_Blood_SH064


title: Mouse_Blood_SH073


title: K208_120min_cR40

value: GAATTCGT-TAATCTTA


title: K210_120min_cR40

value: GAATTCGT-GTACTGAC


title: K202_120min_cR40

value: GAATTCGT-AGGCGAAG


title: K215_120min_cR40

value: TAATGCGC-GGCTCTGA


title: Mouse_Blood_SH067


title: K214B_120min_cR40

value: TAATGCGC-CCTATCCT


title: Mouse_Blood_SH063


title: K158_60min_cR41


title: K157_60min_cR41


title: K152_60min_cR41

value: GAATTCGT-ATAGAGGC


title: K154_60min_cR41

value: GAATTCGT-GGCTCTGA


title: Mouse_Blood_SH059

value: BALB/cByJ

value: Blood


title: Mouse_Blood_SH065

value: Female


title: Mouse_Blood_SH061


title: Mouse_Blood_SH062


title: Mouse_Blood_SH058

value: Male


title: K147_60min_cR41

value: mushroom body

value: GAGATTCC-CAGGACGT


title: K151_60min_cR41

value: K

value: GAATTCGT-TATAGCCT


title: K150_60min_cR41

value: GAGATTCC-GTACTGAC


title: K141_60min_cR41

value: GAGATTCC-TAATCTTA


title: K134_60min_cR02

value: AGCGATAG-TATAGCCT


title: Mouse_Blood_SH057


title: K132_60min_cR02

value: AGCGATAG-CAGGACGT


title: K133_60min_cR02

value: AGCGATAG-GTACTGAC


title: Mouse_Blood_SH045


title: K131_60min_cR02

value: AGCGATAG-TAATCTTA


title: K125_60min_cR02

value: AGCGATAG-GGCTCTGA


title: K127_60min_cR02

value: AGCGATAG-AGGCGAAG


title: Mouse_Blood_SH041


title: K124_60min_cR02

value: AGCGATAG-CCTATCCT


title: K123_60min_cR02

value: AGCGATAG-ATAGAGGC


title: K155_60min_cR41

value: GAATTCGT-AGGCGAAG


title: K153_60min_cR41

value: GAATTCGT-CCTATCCT


title: Mouse_Blood_SH040

value: BALB/cByJ

value: Blood

value: Male


title: K138_60min_cR02

value: K

value: mushroom body


title: K121B_60min_cR02


title: Mouse_Blood_SH039


title: K114_60min_cR40

value: GAATTCGT-TATAGCCT


title: Mouse_Blood_SH056


title: K112B_60min_cR40

value: GAGATTCC-CAGGACGT


title: Mouse_Blood_SH038


title: Mouse_Blood_SH037


title: K113B_60min_cR40

value: GAGATTCC-GTACTGAC


title: K116_60min_cR40


title: Mouse_Blood_SH036


title: Mouse_Blood_SH035

value: Female


title: K110B_60min_cR40

value: GAGATTCC-AGGCGAAG


title: K103_60min_cR40

value: GAGATTCC-CCTATCCT


title: K059_30min_cR41


title: K111B_60min_cR40

value: GAGATTCC-TAATCTTA


title: K058_30min_cR41

value: GAGATTCC-GGCTCTGA


title: Mouse_Blood_SH034


title: K054_30min_cR41

value: GAGATTCC-TATAGCCT


title: K056_30min_cR41

value: GAGATTCC-ATAGAGGC


title: K057_30min_cR41


title: GES15-04917-774

value: Collaborative Cross strains, were developed by crossing eight unique and genetically diverseinbred mouse strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ

value: Kidney


title: Mouse_Blood_SH033

value: BALB/cByJ


title: Mouse_Blood_SH030

value: Blood


title: K053_30min_cR41

value: TCCGGAGA-GTACTGAC


title: K119_60min_cR40

value: K

value: GAATTCGT-GGCTCTGA


title: K109_60min_cR40

value: mushroom body


title: Mouse_Blood_SH020

value: Male


title: K046_30min_cR41

value: TCCGGAGA-TAATCTTA


title: K050_30min_cR41

value: TCCGGAGA-CAGGACGT


title: Mouse_Blood_SH019


title: K115_60min_cR40

value: GAATTCGT-ATAGAGGC


title: K037_30min_cR02

value: TCCGCGAA-GGCTCTGA


title: K036_30min_cR02

value: TCCGCGAA-GTACTGAC


title: K038_30min_cR02

value: TCCGCGAA-AGGCGAAG


title: Mouse_Blood_SH018


title: Tac1 d4 2 scRNA-seq

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

description: EECs sorted for reporter positivity. All columns are d4 BMP4 treated EECs.

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutt files contain UMI barcode normalised abundance counts

source_name: Experiment3 C57/BL6 mice

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Live cells positive for the hormone reporter were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

value: Tac1 reporter

value: Murine intestinal organoids

tag: treatment

value: d4 BMP4 treated


title: K034_30min_cR02

value: TCCGCGAA-ATAGAGGC


title: Mouse_Blood_SH016

value: BALB/cByJ


title: K030_30min_cR02

value: TCCGCGAA-CAGGACGT


title: Tac1 24h scRNA-seq

description: EECs sorted for reporter positivity. All columns are 24hr BMP4 treated EECs.

value: 24hr BMP4 treated


title: K033_30min_cR02

value: K

value: TCCGCGAA-TATAGCCT


title: K028_30min_cR02

value: mushroom body

value: TAATGCGC-CAGGACGT


title: mOSN_Ldb1KO_RNAseq_rep4

source_name: mature olfactory sensory neurons

tag: genotype/variation

tag: tissue/cell type

value: mature olfactory sensory neurons


title: K019_30min_cR40

value: GAGATTCC-ATAGAGGC


title: Tac1-Cre 1 scRNA-seq

description: EECs sorted for reporter positivity. Columns 1-6 are BMP4 untreated, columns 7-12 are 24hr BMP4 treated, columns 13-24 are d4 BMP4 treated EECs (see readme text file)

value: see readme.txt (untreated, 24h BMP4 treated, 4d BMP4 treated)


title: K039_30min_cR02

value: TCCGCGAA-TAATCTTA


title: K018_30min_cR40

value: GAGATTCC-TATAGCCT


title: Mouse_Blood_SH015

value: Blood

value: Female


title: K043_30min_cR41

value: TCCGGAGA-AGGCGAAG


title: Mouse_Blood_SH014


title: K014_30min_cR40

value: TCCGGAGA-CAGGACGT


title: K017_30min_cR40

value: TCCGGAGA-GTACTGAC


title: Mouse_Blood_SH013

value: BALB/cByJ


title: K035_30min_cR02

value: TCCGCGAA-CCTATCCT


title: Mouse_Blood_SH017

value: Male


title: K013_30min_cR40

value: K

value: TCCGGAGA-TAATCTTA


title: Mouse_Blood_SH012


title: mOSN_3EnhKO_RNAseq_rep4

value: OMP-IRES-GFP; H-/-; Lipsi-/-; Sfaktiria-/-


title: K012_30min_cR40

value: mushroom body


title: mOSN_Ldb1KO_RNAseq_rep3

value: mature olfactory sensory neurons


title: Mouse_Blood_SH011


title: K023B_30min_cR02

value: TAATGCGC-GTACTGAC


title: K010_30min_cR40

value: TCCGGAGA-CCTATCCT


title: Tac1 d4 1 scRNA-seq

value: Tac1 reporter

value: Murine intestinal organoids

value: d4 BMP4 treated


title: mOSN_3EnhKO_RNAseq_rep3


title: K009_30min_cR40

value: TCCGGAGA-ATAGAGGC


title: Mouse_Blood_SH009

value: Blood


title: Mouse_Blood_SH010


title: Chol_Orgs_in_Hep_Medium

first: Huili

last: Hu

address: Upsalalaan 8

description: Murine cholangiocytes organoids in Hep-Medium

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4or 8 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb or coutt files contain UMI barcode normalised abundance counts; ‘bc_celseq2.csv’ file includes all the barcode for each cell ID; readme.txt contains the information about in which column number you could find the proper 1 or 2 samples.

source_name: Liver organoids

growth_protocol: Isolated hepatocytes were filtered by 70um filter, washed twice with cold AdDMEM/F12, counted and mixed with MatrigelR in suspension plates (Greiner). 20,000-50,000 cells were used per well of a 24 well plate. After MatrigelR was solidified, Hep-Medium was added. Hep-Medium consists of AdDMEM/F12 (Thermo Scientific, with Hepes, GlutaMax and Penicillin-Streptomycin ) plus 15% RSPO1 conditioned medium (home-made), B27 (minus vitamin A), 50ng/ml EGF (Peprotech), 1.25mM N-acetylcysteine (Sigma), 10 nM gastrin (Sigma), 3um CHIR99021 (Sigma), 25ng/ml HGF (Peprotech), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Peprotech), 1uM A83-01 (Tocris), 10 mM Nicotinamide (Sigma), and 10uM Rho Inhibitor -27632 (Calbiochem). 14 days after seeding, organoids were mechanically fragmented and re-seeded into new MatrigelR. During culturing, medium was refreshed at most every three days. Organoids are usually passaged with a split ratio of 1:3 every 7-10 days.

extract_protocol:
Hepatocytes were isolated by two steps of collagenase perfusion. Organoids were withdrawn from Matrigel. For bulk sequencing, mRNA were isolated by trizol method according to manufacter's protocol. RNA-sequencing libraries were prepared based on the DESeq2 method (Hashimshony et al., 2016; Love et al., 2014). For single cell sequencing, Organoids were digested by triple into single cells. Live positive single cells were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 8bp random molecular barcode (UMI), a cell-specific barcode, the 5'Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq 500 using 75bp paired end sequencing.

treatment_protocol: No treatment

tag: strain background

value: C57/BL6 mice Chol-Orgs

value: cholangiocytes organoids (Chol-Orgs)


title: Mouse_Blood_SH008


title: rps22a/+ rps22b/+ 4665-mRNA RPKM

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
mRNA
rps22a/+ rps22b/+ 4665-mRNA from total RNA-seq
TotRNA-seq RPL RPS

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations
Supplementary_files_format_and_content: TotRNA-seq RPL RPS: mRNA abundance measurements
Supplementary_files_format_and_content: Rib prof RPL RPS: fp abundance measurements

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Strains were grown in YEPD(2%) at 30C, with shaking.

extract_protocol:
For ribosome profiling, cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009. For mRNA, cells were flash frozen and lysed using hot acid phenol and SDS as described in Ingolia et al., Science, 2009
As described in Ingolia et al, Science 2009

treatment_protocol: Cells were harvested in exponential growth phase (OD600=0.6)


title: Murine_Chol_Orgs_sc

description: single cell sequencing from murine cholangiocyte organoids


title: rps22a 4659-mRNA RPKM

description:
mRNA
rps22a 4659-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Mouse_Blood_SH007


title: K008_30min_cR40

value: TCCGGAGA-TATAGCCT


title: Mouse_Blood_SH006


title: rps25a rps25b 7463-mRNA RPKM

description:
mRNA
rps25a rps25b 7463-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: PHx_Hep_2_and_3

description: primary adult murine hepatocytes isolated from mouse 2 and 3 on the 3rd day after hemihepatectomy

source_name: Murine liver

value: C57/BL6 mice

value: Liver; murine hepatocyte


title: rps22a 4662v-mRNA RPKM

description:
mRNA
rps22a 4662v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: PHx_Hep_1

description: primary adult murine hepatocytes isolated from mouse 1 on the 3rd day after hemihepatectomy


title: rps25b 4658v-mRNA RPKM

description:
mRNA
rps25b 4658v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: K011_30min_cR40

value: K

value: TCCGGAGA-GGCTCTGA


title: rps28a 4472v-mRNA RPKM

description:
mRNA
rps28a 4472v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Mouse_Blood_SH005

value: Female


title: WT2 4484-2-mRNA RPKM

description:
mRNA
WT2 4484-2-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: WT1 4484-1-mRNA RPKM

description:
mRNA
WT1 4484-1-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Mouse_Blood_SH001


title: mouse_Heps_2_3_and_4

description: primary adult murine hepatocytes_2_3_4


title: rpl7a 7962-mRNA RPKM

description:
mRNA
rpl7a 7962-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Murine_hepatocyte_organoids_1_and_2_P3

description: Murine hepatocyte organoids 1 and 2 at passage 3

value: C57/BL6 mice Hep-Orgs

value: hepatocyte organoids (Hep-Orgs)


title: rpl24a 7469-mRNA RPKM

description:
mRNA
rpl24a 7469-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Mouse_Adipose_SH056

source_name: Adipose

value: BALB/cByJ

value: Adipose

value: Male


title: rps29b 4480v-mRNA RPKM

description:
mRNA
rps29b 4480v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl40a 7889-mRNA RPKM

description:
mRNA
rpl40a 7889-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Murine_cholangiocytes_organoids_3_and_hep_org_in_chol_meidum

description: Murine cholangiocytes organoids 3 at passage 5 and Hep-Orgs in Chol-Medium

value: C57/BL6 mice Liver-Orgs

value: liver organoids (Liver-Orgs)


title: rpl7a/+ rpl7b/+  2435-mRNA RPKM

description:
mRNA
rpl7a/+ rpl7b/+  2435-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Mouse_Adipose_SH055


title: Mouse_Adipose_SH054


title: rpl40b 2700-mRNA RPKM

description:
mRNA
rpl40b 2700-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl24b 7465-mRNA RPKM

description:
mRNA
rpl24b 7465-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Murine_hepatocyte_organoids_3_P1

description: Murine hepatocyte organoids 3 at passage 1


title: Murine_cholangiocytes_organoids_1_and_2

description: Murine cholangiocytes organoids 1 and 2 at passage 12


title: Murine_hepatocyte_organoids_1_and_2_P7

description: Murine hepatocyte organoids 1 and 2 at passage 7


title: Mouse_Adipose_SH053


title: rpl26a/+ rpl26b/+ 4654v-mRNA RPKM

description:
mRNA
rpl26a/+ rpl26b/+ 4654v-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: rpl26a rpl26b 5048-mRNA RPKM

description:
mRNA
rpl26a rpl26b 5048-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: Murine_hepatocyte_organoids_1 and_2_P1

description: Murine hepatocyte organoids 1 and 2 at passage 1


title: Mouse_Adipose_SH051


title: Uninjured sciatic nerve, mesenchymal cells (myelin removal beads)

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

country: Canada

institute: Hospital for Sick Children

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Drop-seq tools (version 1.12, http://mccarrolllab.com/dropseq/) with settings as described in the Drop-seq Alignment Cookbook (version 1.2 Jan2016, http://mccarrolllab.com/dropseq/).
The number of cell barcodes per sample was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
A total of 4300 barcodes were selected for the bead treated injured nerve dataset, 2000 barcodes for the FACS sorted nerve dataset, and 880 barcodes for the uninjured nerve dataset (predicted mesenchymal cells only).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw digital gene expression for each sample. Two processed data files are included for the myelin removal bead treated injured nerve sample: one containing all data for all cells and one containing only cells predicted as mesenchymal in origin. A processed data file for all cells is included for the FACS sorted injured nerve. Predicted mesenchymal cells only are included for the uninjured nerve processed data.

source_name: Sciatic nerve

extract_protocol:
Cells were extracted from the sciatic nerves of adult CD1 mice. Nerves were dissociated with collagenase and trypsin and cells were either FACS sorted or processed through myelin removal beads prior to collection of single-cell transcriptomes as described by Macosko et al., 2015, Cell. Injured sciatic nerve samples were isolated from the distal segment 9 days following nerve resection.
Standard Illumina libraries were generated as described by Macosko et al., 2015, Cell.

value: sciatic nerve

value: adult

value: Wildtype CD1


title: Mouse_Adipose_SH050


title: Sciatic nerve, 9 days post injury, (FACS sorted)

extract_protocol:
Cells were extracted from the sciatic nerves of adult CD1 and C57BL/6 mice. Nerves were dissociated with collagenase and trypsin and cells were either FACS sorted or processed through myelin removal beads prior to collection of single-cell transcriptomes as described by Macosko et al., 2015, Cell. Injured sciatic nerve samples were isolated from the distal segment 9 days following nerve resection.
Standard Illumina libraries were generated as described by Macosko et al., 2015, Cell.

value: distal sciatic nerve

value: CD1 and C57BL/6


title: Mouse_Heps_1

description: primary adult murine hepatocytes_1

value: C57/BL6 mice

value: Liver


title: rps0b 4651-fp RPKM

description:
ribosome footprints
rps0b 4651- ribosome footprints
Rib prof RPL RPS


title: Mouse_Adipose_SH052


title: Sciatic nerve, 9 days post injury, (myelin removal beads)


title: Mouse_Adipose_SH049


title: rps28b 4474-fp RPKM

description:
ribosome footprints
rps28b 4474- ribosome footprints
Rib prof RPL RPS


title: Mouse_Adipose_SH048


title: rpl41b 7461-mRNA RPKM

description:
ribosome footprints
rpl41b 7461-mRNA from total RNA-seq
TotRNA-seq RPL RPS


title: second plate of undamaged hepatocytes

description:
Undamaged hepatocytes
B2

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair (R2) was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read (R1) contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: count files contain UMI barcode normalised abundance counts. The file bc_celseq2.csv contains the cell barcode sequence for each column header in the processed data files and is available on series record.

source_name: Undamaged hepatocytes

extract_protocol:
Hepatocytes were isolated by two steps of collagenase perfusion. Live positive single cells (Tomato positive sorting) were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5'Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Mice from 6-24 weeks were treated with Tamoxifen injection 7 days before partial hepatectomy to mark all hepatocytes and will then be performed 2/3 surgery.

value: Albumin-CreERT2; Rosa26-LSL-tdTomato


title: Mouse_Adipose_SH047


title: first plate of undamaged hepatocytes

description:
Undamaged hepatocytes
B1


title: Mouse_Adipose_SH046


title: second plate of hepatocytes from PHx model

description:
Hepatocytes three days after liver hepatectomy
A2


title: first plate of hepatocytes from PHx model

description:
Hepatocytes three days after liver hepatectomy
A1


title: Mouse_Adipose_SH045


title: Mouse_Adipose_SH044


title: Mouse_Adipose_SH043


title: Mouse_Adipose_SH041


title: Mouse_Adipose_SH042


title: Mouse_Adipose_SH039


title: rpl41a 7467-fp RPKM

description:
ribosome footprints
rpl41a 7467- ribosome footprints
Rib prof RPL RPS


title: rpl26b 2374-fp RPKM

description:
ribosome footprints
rpl26b 2374- ribosome footprints
Rib prof RPL RPS


title: Mouse_Adipose_SH038


title: Mouse_Adipose_SH037


title: rpl26a3851-fp RPKM

description:
ribosome footprints
rpl26a3851- ribosome footprints
Rib prof RPL RPS


title: Mouse_Adipose_SH036


title: Mouse_Adipose_SH040


title: rpl40a/+ rpl40b/+ 3654v-fp RPKM

description:
ribosome footprints
rpl40a/+ rpl40b/+ 3654v- ribosome footprints
Rib prof RPL RPS


title: rpl41b 7461-fp RPKM

description:
ribosome footprints
rpl41b 7461- ribosome footprints
Rib prof RPL RPS


title: rpl38 3853v-fp RPKM

description:
ribosome footprints
rpl38 3853v- ribosome footprints
Rib prof RPL RPS


title: Mouse_Adipose_SH035


title: Mouse_Adipose_SH034


title: 251485047658_1_1

first: Slava

last: Epelman

state: Ontario

address: 101 College St

department: Cardiology, University Health Network

institute: Toronto General Hospital Research Institute

description: Chip: 7

hyb_protocol: Gene Expression hybridization buffer, Agilent 10X Blocking agent and Kreatech Kreablock. The hybridization solutions were applied to Agilent Human 4x44K V1 microarrays. Hybridization was carried out at 65oC for 20hrs. Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent SureScan microarray scanner to detect Cy5 fluorescence. Gridding and analysis of images was performed using Agilent Feature Extraction v10.7.3.1.

data_processing: Background subtracted, log transformed, quantile normalized data were analyzed using ANOVA testing with contrasts (Partek GS, Partek, St. Louis, MO).

source_name: Heart

label_protocol: Kreatech Cy5-ULS

extract_protocol: RNA was extracted using Qiagen RNA extraction kit (Mini)

value: heart

tag: sorted cell population

value: MHC-II Hi Macrophage


title: 251485047658_1_2

description: Chip: 7

value: CCR2+ Macrophage


title: 251485047658_1_4

description: Chip: 7


title: 251485047657_1_3

description: Chip: 6

value: CCR2+ Monocyte


title: 251485047657_1_1

description: Chip: 6


title: 251485047657_1_2

description: Chip: 6


title: 251485047658_1_3

description: Chip: 7


title: 251485047657_1_4

description: Chip: 6


title: 251485047656_1_4

description: Chip: 5


title: HLE-gln free-U0126-24h-rep2

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data was analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human HuGene-2_0-st-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: HLE cells cultured in glutamine-free media containing 20 µM U0126

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: The cells were grown under normal cell culture conditions prior to treatment.

extract_protocol: RNA was isolated using InviTrap Spin Universal RNA Mini Kit (Stratec Biomedical AG, Germany) according to manufacturer’s instruction.

treatment_protocol: After overnight incubation, the cells were further cultured for 24 hours in complete media, glutamine-free media or glutamine-free media containing U0126.

tag: cell line

value: hepatocellular carcinoma cell line HLE


title: HLE-gln free-24h-rep2

source_name: HLE cells cultured in glutamine-free media

value: gln (short form for glutamine) free media


title: HLE-complete media-24h-rep1

source_name: HLE cells cultivated in culture media supplemented with glutamine

value: Routine cell culture media supplemented with glutamine


title: HLE-gln free-U0126-24h-rep1


title: HLE-complete media-24h-rep2


title: Mouse_Adipose_SH032

extract_protocol: (UCLA Data) For each sample 50-100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and dA-tailing was performed by the addition of Klenow Fragment 3’->5’ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP and d5mCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 2 µl of Illumina Ligation Mix 2 (Illumina, TruSeq Nano cat# FC-121-4001). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 300 bp. Bisulfite treatment was performed using Epitect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer's protocol, except that two consecutive rounds of conversion are performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30s; 12 cycles of 98°C for 15s, 60°C for 30s, 72°C for 30s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers. Libraries were sequenced 100 bp single-end on an Illumina HiSeq4000.

value: BALB/cByJ

value: Adipose

value: Female


title: HLE-gln free-24h-rep1


title: 251485047656_1_2

description: Chip: 5


title: Mouse_Adipose_SH031


title: Mouse_Adipose_SH033


title: Mouse_Adipose_SH030

value: Male


title: Mouse_Adipose_SH029


title: 251485047656_1_1

description: Chip: 5


title: Mouse_Adipose_SH028


title: Mouse_Adipose_SH026


title: 251485047655_1_3

description: Chip: 4


title: 251485047655_1_4

description: Chip: 4


title: Mouse_Adipose_SH027


title: MHCC-97H-SH-UCK2-B-1

city: Guangzhou

first: Shanzhou

last: Huang

address: No. 58 Zhongshan Second Road

institute: First Affiliated Hospital of Sun Yat-sen University

description:
U1
MHCC-97H-SH-UCK2-B-1

data_processing:
Sequenced reads were aligned to hg38-ref-mRNA using tophat/2.0.14-gcc-4.8.5
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated using Htseq
Different expression genes were calculated by DESeq (Anders et al,2010) edgeR package, |log2(FoldChange)| > 1 ,Pvalue < 0.05,"https://bioconductor.org/biocLite.R"
Genome_build: hg38
Supplementary_files_format_and_content: TPMs

source_name: MHCC-97H  liver cancer cells, SH-UCK2

growth_protocol: knocking down UCK2 in MHCC-97H cell

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: knocking down UCK2 in MHCC-97H cell

value: MHCC-97H  liver cancer cells

value: UCK2 knockdown


title: MHCC-97H-SH-UCK2-B-2

description:
U2
MHCC-97H-SH-UCK3-B-2


title: Mouse_Adipose_SH024

data_processing:
All raw sequence files were processed using the BS_Seeker2 software in RRBS mode with standard parameters
Final processed files used in the analysis were modified from the BS_Seeker2 output files (".CGmap") to generate "CGfinal" files.
CGfinal files: For each CpG site in each sample we estimated the methylation frequency as the number of methylated mapped read counts over the total mapped read counts.  Where available, the counts for the forward and reverse Cytosines of the CpG were pooled and treated as a single measurement.  We then computed a 95% confidence interval with a Bayesian approach [64] using a Beta distribution (0.5,0.5) (“Jeffrey’s Prior”) for all methylation values [65]
Genome_build: mm10
Supplementary_files_format_and_content:  [CGfinal files]  chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency


title: Mouse_Adipose_SH025


title: MHCC-97H-SH-NC-2

description:
N2
MHCC-98H-SH-NC-2

source_name: MHCC-97H  liver cancer cells, SH-NC

value: control


title: 251485047656_1_3

description: Chip: 5


title: 251485047655_1_1

description: Chip: 4


title: MHCC-97H-SH-NC-1

description:
N1
MHCC-97H-SH-NC-1


title: Mouse_Adipose_SH023


title: Mouse_Adipose_SH022


title: 251485047655_1_2

description: Chip: 4


title: 251485047654_1_4

description: Chip: 3


title: Mouse_Adipose_SH021


title: Mouse_Adipose_SH019


title: Mouse_Adipose_SH020


title: Mouse_Adipose_SH018


title: A549 poly-IC 1 h

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

description:
WTpIC-1h
Lipofectamine-based transfection of 1 ug/mL poly-IC 1 h
Sample 3 - A549 poly-IC 1 h

data_processing:
Reads were split by barcodes and assigned to the respective samples
Reads were mapped to HG19 using TopHat 2 set to map first stranded reads with default parameters
Exon reads were counted using HTseq-count in union mode
Read counts were normalized using information about the number of PCR cycles used for library prep. This normalization was cross-checked using reads mapping to the Drosophila melanogaster genome in each sample. Because equal amounts of Drosophila melanogaster RNA was spiked into each sample at the beginning of library prep, the drift in drosophila RNA reads matched perfectly with the difference in PCR cycles used for library prep
Genome_build: HG19
Supplementary_files_format_and_content: Excel sheet with exon counts

molecule: polyA RNA

source_name: A549 poly-IC

growth_protocol: Grown in RMPI supplemented with 10% FBS

extract_protocol:
At the endpoint, media was aspirated and cells were lysed in 300 uL RLT buffer (RNeasy extraction kit, Qiagen) and total RNA was extracted. RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies). 10 ng Drosophila melanogaster total RNA was spiked into each sample.
The mRNA was enriched by oligo-dT pulldown from total RNA, followed by fragmentation, adapter ligation, PCR amplification, and finally sequencing on Illumina HiSeq 2000 platform.

treatment_protocol: A549 cells in a 12-well plate were transfected with 1 ug/mL poly I:C using Lipofectamine 2000 as per manufracturer's instructions. Treatment durations were 0.5, 1, 2, 4 h.

value: Lung carcinoma epithelium cells

tag: cell phenotype

value: Adherent


title: A549 poly-IC 4 h

description:
WTpIC-4h
Lipofectamine-based transfection of 1 ug/mL poly-IC 4 h
Sample 5 - A549 poly-IC 4 h


title: A549 poly-IC 2 h

description:
WTpIC-2h
Lipofectamine-based transfection of 1 ug/mL poly-IC 2 h
Sample 4 - A549 poly-IC 2 h


title: A549 lipofectamine alone

description:
WTlipo
Lipofectamine mock transfection 4 h
Sample 1 - A549 lipofectamine alone

source_name: A549 lipofectamine alone


title: Mouse_Adipose_SH017


title: A549 poly-IC 0.5 h

description:
WTpIC-0.5h
Lipofectamine-based transfection of 1 ug/mL poly-IC 0.5 h
Sample 2 - A549 poly-IC 0.5 h


title: Mouse_Adipose_SH016


title: 251485047654_1_3

description: Chip: 3


title: Mouse_Adipose_SH015


title: Mouse_Adipose_SH014


title: Mouse_Adipose_SH011


title: Mouse_Adipose_SH012


title: Mouse_Adipose_SH013


title: Mouse_Adipose_SH006


title: Mouse_Adipose_SH009


title: Mouse_Adipose_SH007


title: Mouse_Adipose_SH004


title: Mouse_Adipose_SH010


title: Il1B-rep2

source_name: Pancreatic beta-cells

value: Tg(ins:IL1B); Tg(ins:mKO)

value: Pancreatic beta-cells

value: 3 months old

value: Interleukin 1B expression in beta cells


title: Mouse_Adipose_SH005


title: Mouse_Adipose_SH003


title: Mouse_Adipose_SH002


title: Il1B-rep1


title: Mouse_Adipose_SH001


title: H4T9rep2

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

data_processing:
ChIP-Nexus reads were aligned to ASM294v2.20 build using Bowtie2, trimmed first 15bp; Input data aligned to ASM294v2.20 build using Bowtie2;
ChIP-Nexus data were analysis using MACE; INPUT data were analysis using samtools and bedtools, Deeptools;
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: Deeptools was used to generate 50bp slides window bw file.

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: Schizosaccharomyces pombe cell were grown in rich medium (1X YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-Nexus libraries were prepared essentially as described in He et al., 2015, Briefly, protein G-dynabeads bound DNA-protein-complexes were affinity selected using specific antibodies . DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment and T4 polynucleotide kinase. A single 3'-A overhang was added using Klenow 3'-5' exo- polymerase. Adapters were ligated and blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim possible 3’ overhangs. Blunted DNA was then sequentially digested by lambda exonuclease and RecJf. Digested single strand DNA was then eluted, reverse cross-linked and phenol-chloroform purified. Fragments were  then self-circularized by Circligase. An oligonucleotide was hybridized to circularized single DNA for subsequent BamHI digestion in order to linearize the DNA. This linearized single strand DNA was then PCR-amplified using adapter sequences and library was purified and size selected using Ampure XP beads. The sequencing libraries were sequenced following Illumina's work flow.

treatment_protocol: For Recombination Induced Tag Exchange experiment (RITE), cells were treated with 1 mM b-estradiol.


title: H4T9rep1


title: H4T6rep1


title: H4T6rep2


title: H4T2rep1


title: H4T2rep2


title: WT_Female_3mo_EFM13_S95: Wild type Cre-

city: Indianapolis

first: Lynda

last: Bonewald

state: IN

address: 635 Barnhill Drive, VanNuys Medical Science Building

institute: Indiana University

data_processing:
The sequencing data were first assessed using FastQC, ver0.11.5 (Babraham Bioinformatics, Cambridge, UK) for quality control.
All sequenced libraries were mapped to the mm10 mouse genome using STAR RNA-seq aligner, ver2.5 with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils, ver0.5.9 (from ngsutils).
Uniquely mapped sequencing reads were assigned to mm10 refSeq genes using featureCounts, ver1.5.1 (from subread) with the following parameters: “-s 2 -p –Q 10”.
Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR, ver3.12.1. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: an excel file include RPKM values for each sample

source_name: Gastrocnemius skeletal muscle

extract_protocol:
Total RNA was extracted from grastrocnemius muscle from 1-month-old Sost-CreERT2 and wild type Cre- male mice and 3-month-old Sost-CreERT2 and wild type Cre- female mice  for RNAseq analysis using a fibrous tissue RNeasy kit (Qiagen) and purified using a MinElute RNA cleanup kit (Qiagen) per the manufacturer’s instructions.  Muscles from both legs were combined for RNA extraction. Extracted RNA samples were stored at -80°C until use.
The concentration and quality of total RNA samples was first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control. Then five hundred nanogram of RNA per sample were used prepare dual-indexed strand-specific cDNA library using TruSeq Stranded mRNA Library Prep Kit (Illumina). The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. Two hundred pico molar pooled libraries were utilized per flowcell for clustering amplification on cBot using HiSeq 3000/4000 PE Cluster Kit and sequenced with 2×75bp paired-end configuration on HiSeq4000 (Illumina) using HiSeq 3000/4000 PE SBS Kit. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

value: Gastrocnemius skeletal muscle

value: female


title: WT_Female_3mo_EFM14_S96: Wild type Cre-


title: H3T9rep1


title: WT_Female_3mo_EFM12_S94: Wild type Cre-


title: Cre_Female_3mo_8619_S92: SostERt2 Cre+


title: Cre_Female_3mo_8617_S93: SostERt2 Cre+


title: H3T9rep2


title: Mouse_Adipose_SH008

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822


title: H3T6rep2


title: WT_Male_1mo_DP3-4_S91: Wild type Cre-

value: male


title: H3T6rep1


title: WT_Male_1mo_DP3-1_S90: Wild type Cre-


title: WT_Male_1mo_DP3-2_S89: Wild type Cre-


title: H3T2rep2


title: Cre_Male_1mo_DQ1-2_S87: SostERt2 Cre+


title: Cre_Male_1mo_DP3-3_S88: SostERt2 Cre+


title: H3T2rep1


title: T6

description: INPUT


title: Cre_Male_1mo_DQ1-1_S86: SostERt2 Cre+


title: T2

description: INPUT


title: YOTA

city: Zhenjiang

first: Kaili

last: Wang

state: Jiangsu

address: Xuefu Road 301

department: School of food and biological engineering

institute: Jiangsu University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million was the value of expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.TPM means transcripts per million,using the formula of R1*1000*1000000/(L1*Rtoatl),R1: The count value of the gene;L1: The length of the gene;Rtotal: the sum value of all the corrected count value .

organism: Yarrowia lipolytica

source_name: Fungus

growth_protocol: Yarrowia lipolytica Y-2 was inoculated in NYDB medium, an was incubated at 28℃， 180 rpm. For 48 h.

extract_protocol:
Yeast were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sample  of Y is the control which no treatment with citrinin, sample YOTA was treated with 1ug/mL OTA

value: Yarrowia lipolytica Y-2 in NYDB medium with OTA

tag: incubation time

tag: incubation conditions


title: C2PD_combined

status: Public on Nov 28 2018

city: Wuhan City

first: Fan

last: Wu

address: Bayi Road No. 299

institute: Wuhan Univwesity

data_processing:
For pull-down data, raw fastq reads were trimmed by cutadapt (v1.14) to remove adapters and mapped to the reference genome GRCm38.p5 and GRCh38.p7 using Bowtie2 (v2.2.9), respectively. Reads with mapping quality less than ten were discarded by SAMtools (v1.3.1), HOMER (v4.9.1) was employed for further process, including peak calling, annotation, and correlation analysis. Tag directories were created and subjected to peak calling in factor mode. Only peaks occuring across replicates were retained for further analysis (fold change cutoff: 5).
Genome_build: GRCm38.p5; GRCh38.p7
Supplementary_files_format_and_content: Peak files contain each peak's coordinate range and correspongding peak score, fold change, etc.

source_name: tissues

extract_protocol: under the instruction of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® DNA Library Prep Kit for Illumina. barcode:AGTTCCGT

value: human thyroid carcinoma


title: C2IN_combined

extract_protocol: under the instruction of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® DNA Library Prep Kit for Illumina. barcode:CCGTCCGC


title: C1IN_combined

extract_protocol: under the instruction of NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® DNA Library Prep Kit for Illumina. barcode:ATGTCAGA


title: C1PD_combined


title: T9

description: INPUT

tag: chip antibody


title: Y

value: Yarrowia lipolytica Y-2 cultured in NYDB medium without OTA