title: sme1-1_4ºC

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

country: Spain

institute: Centro de Investigaciones Biologicas

data_processing:
The original image data produced by the sequencer (Illumina HiSeq2000) was transferred into sequences, which were defined as “raw reads” (or “raw data”) and saved as “.fastq” files.
Raw data was cleaned removing adaptor sequences, reads with a percentage of unknown Ns greater than 5% and low quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastq" files.
Reads were mapped to reference Arabidopsis genome TAIR10 release using SOAP2 software (Li et al, 2009). No more than five mismatches per read were allowed.
The gene expression level was calculated using the RPKM method (Mortazavi et al, 2008) using uniquely mapped reads.
Genome_build: TAIR10.
Supplementary_files_format_and_content: Text files includes the number of uniquely mapped clean reads, length, coverage  and the corresponding estimation of expression level (RPKM) for each gene model.

organism: Arabidopsis thaliana

source_name: leaves from two-week-old plants_sme1-1_4C

growth_protocol: Plants were grown under long-day photoperiods (photon flux of 90 µmol m-2 s-1) on soil.

extract_protocol:
Leaf tissue was colected, inmediately frozen on liquid nitrogen and stored at -80ºC. For total RNA extraction, frozen tissue was homogenized to a fine powder and total RNA was extracted using TRIzol® Reagent (Life Technologies), treated with DNaseI (Roche) and further cleaned with RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cold treatment was achive by exposing plants to 4ºC for 24h under long-day photoperiods (photon flux of 40 µmol m-2 s-1).

tag: developmental stage

value: two-week-old

value: leaves

tag: background ecotype

tag: genotype


title: Plasma Sample 1 condition 5 rep1

status: Public on Jan 31 2019

type: SRA

city: San Francisco

first: Cassandra

middle: D

last: Belair

state: CA

address: 35 Medical Center Way

department: Urology

country: USA

institute: UCSF

description:
CB02_4N43_43N100
3' adapter 0.2uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt

library_source: transcriptomic

data_processing:
Demultiplex: CutAdapt v1.11 --no-trim -e 0 -O 20
Trim adapters: CutAdapt v1.11 -u 4 -m 17 -e 0 -O 20
Align to custom genomes using bowtie v1.1.2 or bowtie2 v2.2.5 sequentially removing adapter/marker "contaminant" sequences, mature miRNA, other small RNAs, then finally to genomic sequences.
bowtie2 --local -L 17 (contaminant genome)
bowtie -n 0 -l 18 --best (all other genomes)
Custom bash script to generate counts.
Custom bash or r scripts to collapse PCR duplicates using UMI.
Genome_build: hg19 (GRCh37) for human genome, small RNAs downloaded from RNACentral Database release5.
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing either counts or sequences.

molecule: total RNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
Qiagen micro miRNeasy kit modified to use 1:7 serum:Trizol or 1:3 serum:Trizol LS.
See manuscript for details.

tag: tissue

value: Plasma

tag: Sex

value: Male


title: Plasma Sample 1 condition 5 rep2

description:
CB02I_4N44_44N100
3' adapter 0.2uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: SenSp5

type: RNA

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
3112_12187_SenSp5
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.

hyb_protocol: Followed Affymetrix standard hybridization protocol for MoGene1.0 arrays.

scan_protocol: Chips were scanned with Affymetrix 7G scanner at the standard setting.

data_processing: The raw chip data files (.CEL) were processed through Affymetrix standard analysis pipeline for RMA background correction, median-polish summarization and quantile normalization. The .CHP files were generated at gene-level.

label: biotin

organism: Mus musculus

source_name: BM-derived cells in spleen

label_protocol: RNAs were amplified with the Nugen Ovation Pico WTA kit to generate cDNA targets labeled with biotin.

growth_protocol: Mice were perfused with 25 mL of ice-cold PBS. Subsequently, brains and spinal cords were collected from perfused mice and homogenized to obtain single cell suspensions. CNS cells were purified by centrifugation for 30 min in a 95% Percoll solution with EBSS.

extract_protocol: RNAs were extracted using Qiagen RNeasy Mini kit.

treatment_protocol: We induced active EAE in standard fashion. Briefly, mice were immunized with residues 35-55 of myelin oligodendrocyte glycoprotein (MOG35-55) emulsified in complete Freund’s adjuvant. 200 ng of pertussis toxin was administered at the time of immunization and two days later.

value: BM-derived cells in spleen

tag: cell type

value: radiation sensitive DCs


title: Plasma Sample 1 condition 6 rep1

description:
CB02_4N46_46N100
3' adapter 0.85uM; 5' adapter 3.3uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 4 rep3

description:
CB02_4N42_42N100
3' adapter 0.05uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Col-0_4ºC

source_name: leaves from two-week-old plants_Col-0_4C

value: WT


title: Col-0_20ºC

source_name: leaves from two-week-old plants_Col-0_20C


title: sme1-1_20ºC

source_name: leaves from two-week-old plants_Sme1-1_20C


title: YF00104_32_BL

city: Cleveland

first: Ali

last: Filali

address: 10900  Euclid Avenue

department: Pathology

institute: CWRU

description:
Pre-vaccination sample
5645692058_D

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized toHumanRefSeq8 V2   BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using  various software packages from R and Bioconductor.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

source_name: Whole blood

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Gene expression microarrays were undertaken using  whole blood samples obtained from 36 subjects

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

tag: baseline nab titer

tag: day84 nab titer

tag: gender

value: M

tag: donor

tag: age


title: YF00104_30_BL

description:
Pre-vaccination sample
5645692049_B

treatment_protocol: Gene expression microarrays were undertaken using  whole blood samples obtained from 36 subjects

value: F


title: SenSp1

description:
3112_12183_SenSp1
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.


title: YF00104_33_BL

description:
Pre-vaccination sample
5645692058_H


title: YF00104_34_BL

description:
Pre-vaccination sample
5645692059_L


title: Plasma Sample 1 condition 4 rep2

description:
CB02_4N41_41N100
3' adapter 0.05uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: YF00104_36_BL

description:
Pre-vaccination sample
5645764038_B


title: Plasma Sample 1 condition 4 rep1

description:
CB02_4N40_40N100
3' adapter 0.05uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: YF00104_31_BL

description:
Pre-vaccination sample
5645692049_J


title: YF00104_29_BL

description:
Pre-vaccination sample
5645692034_L


title: YF00104_35_BL

description:
Pre-vaccination sample
5645764008_D


title: Plasma Sample 1 condition 3 rep3

description:
CB02_4N38_38N30
3' adapter 0.85uM; 5' adapter 1.0uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: YF00104_27_BL

description:
Pre-vaccination sample
5645692022_L


title: Plasma Sample 1 condition 2 rep1

description:
CB02_4N25_25N10
3' adapter 0.85uM; 5' adapter 0.33uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 2 rep2

description:
CB02_4N26_26N10
3' adapter 0.85uM; 5' adapter 0.33uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 3 rep1

description:
CB02_4N36_36N30
3' adapter 0.85uM; 5' adapter 1.0uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: YF00104_28_BL

description:
Pre-vaccination sample
5645692034_D


title: Plasma Sample 1 condition 1 rep3

description:
CB02_4N09_09M
3' adapter 0.85uM; 5' adapter 3.3uM modified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 1 rep2

description:
CB02_4N08_08M
3' adapter 0.85uM; 5' adapter 3.3uM modified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 1 rep1

description:
CB02_4N07_07M
3' adapter 0.85uM; 5' adapter 3.3uM modified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Plasma Sample 1 condition 3 rep2

description:
CB02_4N37_37N30
3' adapter 0.85uM; 5' adapter 1.0uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: Human coronary arterial endothelial cells (HCAEC) 4

city: MEXICO

first: Angélica

middle: Rangel

last: López

state: Cuauhtémoc

address: Avenida Cuauhtémoc 330

country: Mexico

institute: IMSS

description: Human coronary arterial endothelial cells (HCAEC) primary cultures exposed to uremic serum from of patients with cardiovascular diseases (CKD) and  myocardial infarction (UCI)

hyb_protocol: The hybridization onto the microarray Genechips in Affymetrix hybridization oven at 60 rpms, 45ºC for 17 hours.

scan_protocol: Scanned at the Affymetrix 7G GeneArrays Scanner.

data_processing: Probe cell intensity data (CEL files) were converted into expression values through a custom pipeline implemented in R language within the Bioconductor environment. Robust Multiarray Average (RMA) algorithm was implemented by execution of background correction followed by a quantile normalization and finished by probe summarization. The LIMMA package (Linear Models for Microarray Data) of the Bioconductor software17 was implemented to identify relevant DEGs between two differential conditions uraemia without infarction (USI) and uraemia with infarction (UCI). Only DEGs with a P-value less than 0.05 were select for further analysis. All previous steps in Affymetrix data preprocessing and DEG analysis were achieved via execution of the in-house script in the R scripting language interface

source_name: Chronic kidney disease (CKD) with myocardial infarction (UCI)

label_protocol: 100 ng RNA total was used in reverse transcribed to cDNA, after was fragmented by enzymatic reaction and biotinylated by enzymatically reaction using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

growth_protocol: Primary Coronary Artery Endothelial Cells; Normal, Human (HCAEC) ATCC®PCS-100-020™ were obtained from ATCC® and supplemented with 20% plasma from patients with uremic group for 72 h.

extract_protocol: RNA was obtained using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. RNA integrity and concentration were measure using a 2100 Bioanalyzer, using the RNA 6000 Nano LabChip kit (Agilent Technologies, Santa Clara, CA, USA) and NanoDrop ND-1000 spectrophotometer, respectively. Only those samples with an RNA integrity number (RIN) ≥ 9.5 were included in microarray analysis

treatment_protocol: The cell lines after treatment were washed with PBS after that were disrupted using a TissueLyserTM system (Qiagen, Valencia, CA, USA) for 25s at 25 Hz.

tag: treatment

value: exposed to uremic serum from patients with chronic kidney disease with  myocardial infarction (USI)


title: Human coronary arterial endothelial cells (HCAEC) 1

description: Human coronary arterial endothelial cells (HCAEC) primary cultures exposed to uremic serum from of patients with cardiovascular diseases (CKD)

source_name: Chronic kidney disease (CKD) without myocardial infarction (USI)

value: exposed to uremic serum from patients with chronic kidney disease without  myocardial infarction (USI)


title: YF00104_24_BL

description:
Pre-vaccination sample
5645692020_F


title: Human coronary arterial endothelial cells (HCAEC) 5


title: YF00104_25_BL

description:
Pre-vaccination sample
5645692020_J


title: Human coronary arterial endothelial cells (HCAEC) 6


title: YF00104_26_BL

description:
Pre-vaccination sample
5645692022_D


title: Control cell 4 24 cycles rep2

description:
TJ12hi_4N02_ccell4_500ng_2
3' adapter 0.05uM; 5' adapter 0.33uM modified.
processed data file: TJ12hi_Mature_counts_raw.txt
processed data file: TJ12hi_Mature_counts_collapsed.txt

source_name: cell line

tag: cell line


title: YF00104_22_BL

description:
Pre-vaccination sample
5645692011_F


title: Human coronary arterial endothelial cells (HCAEC) 3


title: YF00104_23_BL

description:
Pre-vaccination sample
5645692020_B


title: Control cell 4 rep2

description:
TJ12_4N02_ccell4_500ng_2
3' adapter 0.05uM; 5' adapter 0.33uM modified.
processed data file: Map_stats_TJ12_trimmed_all.txt
processed data file: TJ12_Mature_counts_raw.txt
processed data file: TJ12_Mature_counts_collapsed.txt
processed data file: TJ12_4N02_ccell4_500ng_2_Mature_collapsed_seqs.txt


title: Human coronary arterial endothelial cells (HCAEC) 2


title: Control cell 4 24 cycles rep1

description:
TJ12hi_4N01_ccell4_500ng_1
3' adapter 0.05uM; 5' adapter 0.33uM modified.
processed data file: TJ12hi_Mature_counts_raw.txt
processed data file: TJ12hi_Mature_counts_collapsed.txt


title: YF00104_21_BL

description:
Pre-vaccination sample
5645692011_B


title: Control cell 4 rep1

description:
TJ12_4N01_ccell4_500ng_1
3' adapter 0.05uM; 5' adapter 0.33uM modified.
processed data file: Map_stats_TJ12_trimmed_all.txt
processed data file: TJ12_Mature_counts_raw.txt
processed data file: TJ12_Mature_counts_collapsed.txt
processed data file: TJ12_4N01_ccell4_500ng_1_Mature_collapsed_seqs.txt


title: Control cell 4 16 cycles

description:
TJ11_4N37_ctrl_cell_4
3' adapter 0.05uM; 5' adapter 0.33uM modified; 16 cycles.
processed data file: TJ11_Mature_counts_raw.txt
processed data file: TJ11_Mature_counts_collapsed.txt


title: YF00104_20_BL

description:
Pre-vaccination sample
5645692008_J


title: YF00104_18_BL

description:
Pre-vaccination sample
5645692008_B


title: YF00104_15_BL

description:
Pre-vaccination sample
5645570009_C


title: YF00104_17_BL

description:
Pre-vaccination sample
5645570009_K


title: YF00104_16_BL

description:
Pre-vaccination sample
5645570009_G


title: YF00104_19_BL

description:
Pre-vaccination sample
5645692008_F


title: YF00104_8_BL

description:
Pre-vaccination sample
5552277097_K


title: YF00104_9_BL

description:
Pre-vaccination sample
5552277099_C


title: YF00104_14_BL

description:
Pre-vaccination sample
5645570008_K


title: YF00104_4_BL

description:
Pre-vaccination sample
5552277044_D


title: YF00104_13_BL

description:
Pre-vaccination sample
5645570008_G


title: YF00104_3_BL

description:
Pre-vaccination sample
5491099057_J


title: 254890810729_1_3: D4 chronic (cured) vs. D4 chronic (cured) acute

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description:
(+) polarity
254890810729_1_3

hyb_protocol: Whole human genome microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSPE wash protocol

scan_protocol: Scanning of microarrays was performed with either 5 µm resolution and XDR setting for 4x44K arrays or 3 µm resolution for 8x60K arrays using a G2505C DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware) and with Bioconductor Gene Spring 12.6.1 software (Agilent Technologies).

source_name: D4 Ctr infection - cured

label_protocol: RNA labeling was performed with the Quick Amp RNA Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Epithelial progenitor isolation from fallopian tube samples and organoid culture was done as previously described (Nat Commun. 2015 Dec 8;6:8989. doi: 10.1038/ncomms9989.)

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol:
For infection with Chlamydia trachomatis D (CtrD) 2 wells of organoids were released from MatrigelTM with cold DPBS, pooled and mechanically disrupted by passing them through a 26xG needle. The fragmented organoids were divided equally into 2 tubes for infection and mock control. After centrifugation (300xg, 5min) and removal of the supernatant, 10µl CtrD (from a frozen stock with 108 IFU/mL as determined by titration on HeLa cells) were added to one tube of the pelleted organoids. The suspension was mixed by pipetting and incubated for 15min at 35°C followed by 5min on ice. The mock control was treated the same, but without addition of CtrD. Finally, 50µL MatrigelTM was added to each tube, the organoids seeded and placed in a humidified incubator at 5% CO2 and 35°C. Splitting of organoids was done every 3-4 weeks. RNA samples were taken at 72h p.i. and 1M p.i.  At 4 months p.i. the infection was cured by applying a mixture of Penicillin (100 U/mL) and Streptomycin (100 µg/mL) to the organoid culture for one week.
After curing, a re-infection was carried out identical to the first infection with mechanical splitting, adding of CtrD to one half of the organoids and mock treatment of the other half. Also, the control organoids that have not been infected with CtrD before were infected and mock treated again. 72h post seeding RNA samples were taken of the now 2x infected (chronic cured acute), chronic infected (chronic cured), acute infected (longterm acute) and the never infected organoids

value: fallopial tube

value: organoid donor 4

tag: progression

value: chronic (cured)

source_name: D4 Ctr infection - cured - Ctr reinfection

value: chronic (cured) acute


title: YF00104_12_BL

description:
Pre-vaccination sample
5645570008_C


title: YF00104_11_BL

description:
Pre-vaccination sample
5645570007_K


title: 254890810729_1_2: D4 long term acute vs. D4 naive (cured)

description:
(-) polarity
254890810729_1_2

source_name: D4 naive - cured - Ctr infection

value: long term acute

source_name: D4 naive - cured

value: naive (cured)


title: 254890810730_1_3: D3 chronic (cured) vs. D3 chronic (cured) acute

description:
(+) polarity
254890810730_1_3

source_name: D3 Ctr infection - cured

value: organoid donor 3

source_name: D3 Ctr infection - cured - Ctr reinfection


title: 254890810730_2_2: D2 long term acute vs. D2 chronic (cured)

description:
(-) polarity
254890810730_2_2

source_name: D2 naive - cured - Ctr infection

value: organoid donor 2

source_name: D2 Ctr infection - cured


title: YF00104_10_BL

description:
Pre-vaccination sample
5645570007_C


title: 254890810730_1_1: D3 naive (cured) vs. D3 long term acute

description:
(+) polarity
254890810730_1_1

source_name: D3 naive - cured

source_name: D3 naive - cured - Ctr infection


title: 254890810729_1_4: D4 chronic (cured) acute vs. D4 chronic (cured)

description:
(-) polarity
254890810729_1_4


title: 254890810729_1_1: D4 naive (cured) vs. D4 long term acute

description:
(+) polarity
254890810729_1_1

source_name: D4 naive - cured - Ctr reinfection


title: 254890810730_1_2: D3 long term acute vs. D3 naive (cured)

description:
(-) polarity
254890810730_1_2


title: YF00104_2_BL

description:
Pre-vaccination sample
5491099057_B


title: 254890810730_2_3: D2 chronic (cured) vs. D2 chronic (cured) acute

description:
(+) polarity
254890810730_2_3

source_name: D2 Ctr infection - cured - Ctr reinfection


title: YF00104_6_BL

description:
Pre-vaccination sample
5552277045_G


title: YF00104_1_BL

description:
Pre-vaccination sample
5491099001_B


title: 254890810730_1_4: D3 chronic (cured) acute vs. D3 chronic (cured)

description:
(-) polarity
254890810730_1_4


title: YF00104_5_BL

description:
Pre-vaccination sample
5552277045_C


title: 254890810730_2_4: D2 chronic (cured) acute vs. D2 chronic (cured)

description:
(-) polarity
254890810730_2_4


title: 254890810730_2_1: D2 chronic (cured) vs. D2 long term acute

description:
(+) polarity
254890810730_2_1


title: PB38_MSC_2_BRCA1+/-

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: BRCA1 haploinsufficiency

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: the data were RMA normalized and analysed with Expression Console

source_name: mesenchymal derived from IPSCs BRCA1+/-

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: mesenchymal differentiation of human IPSCs

extract_protocol: Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

value: mesenchyme derived from peripheral blood IPSC


title: YF00104_7_BL

description:
Pre-vaccination sample
5552277045_K

source_name: Whole blood


title: HOC621 EV

city: Tokushima

first: Yasusei

last: Kudo

address: 3-18-15 Kuramoto

department: Institute of Biomedical Sciences

country: Japan

institute: Tokushima University Graduate School

description: Gene expression data from empty vector transfected HOC621 cells

hyb_protocol: Following fragmentation, 3.5 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HuGene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000EX.

data_processing: The data were analyzed with GeneSpring version 14.9.1 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HOC621 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Sigma-Aldrich, St. Louis, MO USA) with 10% fetal bovine serum (FBS, Gibco BRL, Grand Island, NY) and 100 U/ml penicillin-streptomycin (Gibco BRL) under conditions of 5% CO2 in air at 37 ˚C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were stably transfected with empty vector, POSTN isoform 3, or POSTN isoform 6.

value: Oral squamous cell carcinoma cell

tag: transfection

value: empty vector


title: sample_998

city: Kansas City

first: Daniel

middle: Paul

last: Heruth

address: 4th Floor PRC, 2401 Gillham Road

department: Pediatrics

institute: Children's Mercy

data_processing:
The raw base calling (.bcl) files were converted to demultiplexed compressed FASTQ files using Illumina’s bcl2fastq v2.17.1.14 software.
TopHat v1.3.0 was used to map RNA-seq reads against the mouse reference genome using default parameters.
Transcript assembly and abundance estimation and comparing expression were conducted with Cufflinks v1.03 and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Cuffdiff was used to calculate statistical significance changes of gene expression.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file of a matrix table generated using Cufflinks v1.0.3 and reported in Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

source_name: ankle

growth_protocol: Mice were aged 10 weeks old at the initiation of the experiment and euthanized at 20 weeks of age.

extract_protocol:
Samples were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina cat. RS-122-2201, San Diego, CA)
Clusters were generated using the   TruSeq Paired-End Cluster Kit v3-cBot-HS (Illumina cat. PE-401-3001, San Diego, CA).
Paired –end sequencing (2x101 cycles) was completed using the TruSeq SBS kit v3-HS (Illumina cat. FC-401-3001, San Diego, CA).

treatment_protocol: Mice were immunized with bovine collagen type II (CII, 100 µg, Chondrex) in Complete Freund's Adjuvant (CFA, 100 µg M. tuberculosis, Chondrex) by intradermal injection at the base of the tail. A collagen booster (100 µg) in Incomplete Freund's Adjuvant (IFA, Chondrex) was administered at day 21.

value: Male

tag: age (weeks)

tag: strain

value: Collagen Induced Arthritis

value: Nampt +/-


title: HOC621 Iso3

description: Gene expression data from Periostin isoform 3 transfected HOC621 cells

value: Periostin isoform 3


title: SOD KO2

city: Rome

first: Viviana

last: M

address: Via A. Scarpa 16

department: SAIMLAL

country: Italy

institute: La Sapienza University of Rome

data_processing:
Kallisto pseudoalignment; kallisto version 0.43.1; kallisto quant -i INDEXFILE -o OUTPUTNAME --single -l 200 -s 20 INPUTFILE.fastq.gz; Index was created using transcriptome GRCm38 (mm10)
Differential gene expression analysis; DESeq2  version 1.20.0
Supplementary_files_format_and_content: Quantification of transcripts from GRCm38 (mm10)

source_name: Gastrocnemius muscle

extract_protocol:
“TruSeq Stranded mRNA Sample Prep kit” (Illumina, San Diego, CA) was used for library preparation. Libraries were processed with Illumina cBot for cluster generation on the flow cell and sequenced on single-end mode at the multiplexing level requested on HiSeq. 2500 (Illumina, San Diego, CA). The Illumina pipeline based on CASAVA version 1.8.2 of the was used to process raw data for both format conversion and de-multiplexing. Standard bioinformatics analysis was provided by the IGA facility. Briefly, the reads produced (on average 56.4 M reads/sample; min 47.6 M, max 76.8 M) were first put through the sequencing pipeline made of base-calling on the Illumina Pipeline, trimming (min length 35) with ERNE and removal of adapter sequences with Cutadapt. Reads were then aligned to GRCm38 reference genome/transcriptome using TopHat. Overall alignment rate was 95% for all the samples. Cuffdiff was used to perform differential expression analysis
Libraries were processed with Illumina cBot for cluster generation on the flow cell and sequenced on single-end mode at the multiplexing level requested on HiSeq. 2500 (Illumina, San Diego, CA).

value: Gastrocnemius muscle

value: 14 week old

tag: genotype/variation

value: SOD1G93A HDAC4fl/fl myogenin;cre

value: male


title: SOD KO1


title: S224E RNAseq, rep1

city: Boston

first: Andrea

middle: June

last: Kriz

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
ChIP-seq: BWA was used to align reads against the mm9 reference genome (68). Alignments were filtered for uniquely mapped reads and duplicates were removed. Input-normalized coverage tracks were generated using SPP (Kharchenko et al., 2008).  To identify prospective CTCF binding sites, we resolved regions of ChIP-Seq tag enrichment. Tag counts were analyzed in a 1 Kb window over the chromosome length with a 200bp step and estimated statistical significance of enrichment of ChIP vs input using negative binomial distribution, with the estimate of the mean based on the tag counts in input, and the size parameter(s) selected based on manual inspection of resulting peak calls. Regions of significant enrichment were generated by merging adjacent significantly enriched windows separated by 1 Kb or less. Broad regions of enrichment were called using SPP (Kharchenko et al., 2008). Genomic location of the resultant 50,749 CTCF and 912 CTCF Ser224-P peaks (z=6) was categorized using CEAS according to RefGene annotation of introns, exons, and UTRs (Shin et al., 2012).  CTCF and CTCF Ser224-P data was visualized using IGV with ENCODE mESC CTCF ChIP-seq (GSM723015) and RNA-seq (GSM723776) data plotted for reference.  Motif search of the ChIP-seq peak datasets (z=6) and logo generation was performed using MEME-ChIP with default parameters (http://meme-suite.org/)
RNA-seq: RNA-seq reads were trimmed using cutadapt with the options -e 0.2 -q 20 -a AGATCGGAAGAGC -m 20 --overlap 12. Trimmed reads were aligned to the mm9 reference genome using TopHat2 as previously described. PCR duplicates were removed and HOMER used to tabulate unique reads mapping to exons of each gene. DESeq2 was then used to identify differentially expressed (DE) genes. DE genes were counted as those with adjusted p-value < 0.01. Only genes with at least one count in one of the four samples were included in the analysis.    For visualizing RNA-seq reads overlapping codon 224 of CTCF, RNA-seq reads were aligned to the CTCF S224E transgene sequence using the same parameters as above and an index of the CTCF S224E transgene sequence generated using bowtie2 with the default parameters. The resulting bam file of aligned reads was then visualized on IGV.    Overrepresentation analysis of upregulated and downregulated DE genes was done using the PANTHER Classification System (http://www.pantherdb.org). Gene symbols for downregulated or upregulated DE genes used as input lists and the gene symbols of all expressed genes (i.e., all genes used in DESeq2 analysis) were used as the reference list.     Metagene plots of ChIP-seq over DE upregulated, downregulated and all genes were generated via CEAS using bigwig files of reads from CTCF or CTCF Ser224-P ChIP-seq (Kharchenko et al., 2008).
Hi-C^2: Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus and cas reference genomes using novoalign and merged into non-allelic Hi-C summary files and filtered using HOMER. To avoid computational complexities arising from normalization of sparse, non-enriched regions in the Hi-C contact map, only Hi-C interactions falling within the capture region were analyzed further. For each capture, a custom script was used to pull out the filtered Hi-C interactions falling within the target region from the HOMER tag directories. Hi-C contact maps of the capture regions were then generated from these HOMER tags using the ‘pre’ command of Juicer tools. The resulting Hi-C contact maps in .hic format were visualized and normalized with the ‘Coverage (Sqrt)’ option in Juicebox . Insulation scores were computed for Hi-C2 datasets as previously described (Crane et al. 2015, Giorgetti et al. 2016) with a few modifications. Briefly, 25kb resolution ‘Coverage (Sqrt)’ normalized Hi-C2 interaction matrices were extracted from Juicebox using the ‘dump’ function of Juicer tools and converted to the cworld matrix format using custom shell and R scripts. Insulation scores were then computed from the cworld matrices using the ‘matrix2insulation.pl’ cworld script and the parameters ‘-v --is 125000 --ids 75000 –im sum’ and manually normalized using the total number of reads falling in the capture region, rather than total number of reads on the chromosome. TAD scores were then calculated from the insulation scores using the ‘insulation2tads.pl’ cworld script with default parameters and the Mecp2 TAD boundaries manually defined as the bins chrX:71200000-71225000 and chrX:71650000-71675000.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: Input-normalized bigWig files (bw)
Supplementary_files_format_and_content: RNA-seq: bigWig files (bw) of fpm values. Raw exonic read counts in each RNA-seq library are summarized in 'counts' .txt files
Supplementary_files_format_and_content: Hi-C^2: Compressed Hi-C matrix (.hic) files for filtered Hi-C reads in the capture region (chrX:70,370,161-71,832,975 ). File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

molecule: polyA RNA

source_name: mESC

growth_protocol: ES cells were grown on γ-irradiated MEF feeders in ES medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX, LIF) with 15% FBS.

extract_protocol:
ChIP-seq: Harvested cells were crosslinked for 5 minutes in 1% formaldehyde.  Crosslinking was quenched by the addition of glycine to 125mM.  Fixed cells were PBS washed and cell pellets were frozen at -80C. Approximately 2x10^7 cells were used per ChIP. Pellets were resuspended in Lysis buffer 1 (25mM HEPES pH 7.5, 25mM EDTA, 0.5% SDS).  Chromatin was sheared in a Qsonica Q800R for 20 minutes at 40% power 30sec on 30sec off at 4C to ~150bp.  After centrifuging away debris, 4 volumes of Lysis buffer 2 (25mM HEPES pH 7.5, 187.5mM NaCl, 1.25% Triton X-100, 0.625% sodium deoxycholate, 6.25% glycerol, 12.5mM sodium pyrophosphate, 12.5mM B-glycerophosphate, 6.25mM NaF, 1.25mM Na3VO4) were added with protease inhibitors (1mM PMSF, 1ug/mL pepstatin, and 1 ug/mL leupeptin).  Sepharose 4B (Sigma-Aldrich) was washed with ChIP Wash Buffer 1 (25mM HEPES pH 7.5, 150mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 5% glycerol, 5mM EDTA, 10mM sodium pyrophosphate, 10mM B-glycerophosphate, 5mM NaF, 1mM Na3VO4, protease inhibitors) and used to preclear the chromatin samples.  25μL/IP Protein G Dynabeads (ThermoFisher) were blocked in ChIP Wash Buffer 1 100ug/mL Acyclovir, 100ug/mL Zalcitabine, 5% Gly-Gly (Sigma-Aldrich). Beads were then washed with ChIP Wash Buffer 1.  Precleared chromatin, 2ug of anti-CTCF or anti-CTCF Ser224-P antibodies (Table 1), and blocked Protein G Dynabeads were incubated together overnight at 4C with rotation.  10% of the precleared chromatin input was also saved.  IP samples were washed with ChIP Wash Buffer 1, then with ChIP Wash Buffer 2 (25mM HEPES pH 7.5, 300mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 5% glycerol, 5mM EDTA, 10mM sodium pyrophosphate, 10mM B-glycerophosphate, 5mM NaF, 1mM Na3VO4, protease inhibitors) and then with TENG (50mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl, 5% glycerol, protease inhibitors).  IPs were incubated for 30minutes at 37C in TENG with 200ug/mL RNase A. 10% Input samples were also treated with 200ug/mL RNase A.  IPs were washed with ChIP Wash Buffer 2 and then TENG.  IPs were then eluted at 65C in Elution Buffer (50mM Tris-HCl pH7.5, 10mM EDTA, 1% SDS).  An equal volume of TE (Tris-HCl pH 8.0, 1mM EDTA) was added to the eluate with 40ug Proteinase K and incubated for 2hrs at 45C.   The input samples were similarly protease treated in parallel.  Both IP and input cross-links were reversed at 65C overnight and then phenol/chloroform/isoamyl alcohol extracted.  The aqueous phase was further chloroform extracted and then alcohol precipitated.  The DNA was suspended in TE.
RNA-seq: RNA was purified by TRIzol (Thermo Fisher) extraction via manufacturer’s instructions. Polyadenylated mRNA was the selected from total cell RNA using oligo(dT) beads (New England BioLabs).
Hi-C^2: In-situ Hi-C was performed as described in Rao et al. (2014): 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads. HYbrid Capture Hi-C (Hi-C^2) probes were designed and hybridization to in-situ Hi-C libraries carried out as described previously (Sanborn et al., 2015). Probe sets were designed to enrich interactions in the region of interest: chrX:70,370,161-71,832,975 (mm9). Briefly, 120 bp probes were designed around the MboI restriction sites in the regions of interest and custom synthesized pools of single stranded oligodeoxynucleotides ordered from CustomArray, Inc. (Bothell, WA). Single stranded DNA oligos were amplified and biotinylated in a MAXIScript T7 transcription reaction (Ambion). The resulting biotinylated RNA probes were hybridized to 250-300 ng of in situ Hi-C libraries for 24 hours at 65C. DNA hybridized to the RNA probes was pulled down by streptavidin beads (Dynabeads MyOne Streptavidin C1, Life Technologies), washed, and eluted.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 12-18 cycles of PCR amplification, depending on library concentration measured by qPCR.

treatment_protocol: Tet-on CTCF S224E mESCs were grown for six days with or without  1ug/mL doxycycline (RNA-seq). Tet-on CTCF, CTCF S224A, and CTCF S224E mESCs were grown for two days with or without 1ug/mL doxycycline (Hi-C^2).

value: ES cell (F1-2.1)

value: CAST/Ei x 129/Sv/Jae

value: Tet-on CTCF S224E

tag: chip antibody


title: S224E RNAseq, rep2

tag: genotype


title: 254890810729_2_2: D2 long term acute vs. D2 naive (cured)

description:
(-) polarity
254890810729_2_2

tag: tissue

value: fallopial tube

value: long term acute

source_name: D2 naive - cured

value: naive (cured)


title: S224E Dox RNAseq, rep2

value: Doxycycline (1ug/mL), 6 days


title: SOD2

value: SOD1G93A HDAC4fl/fl


title: S224E Dox RNAseq, rep1


title: PB30_MSC_2_BRCA1+/+

description: normal locus

source_name: mesenchymal derived from IPSCs Healthy donor

value: mesenchyme derived from peripheral blood IPSC


title: PB38_MSC_1_BRCA1+/-

description: BRCA1 haploinsufficiency


title: CTCF Ser224-P ChIP DNA, rep1

library_source: genomic

molecule: genomic DNA

value: ES cell (Tsix-stop)

value: Wild-type

value: Rabbit anti-Phospho-CTCF (Ser224) (Cell Signaling Technology, this study)


title: SOD1


title: HOC621 Iso6

description: Gene expression data from Periostin isoform 6 transfected HOC621 cells

value: Oral squamous cell carcinoma cell

value: Periostin isoform 6


title: 254890810729_2_1: D2 naive (cured) vs. D2 long term acute

description:
(+) polarity
254890810729_2_1

value: organoid donor 2


title: 254890810729_2_3: D2 chronic (cured) vs. D2 chronic (cured) acute

description:
(+) polarity
254890810729_2_3

value: chronic (cured)

value: chronic (cured) acute


title: sample_406

tag: Sex

value: Male

value: Collagen Induced Arthritis

value: Nampt +/+


title: sample_45

value: Control

value: Nampt +/-


title: JP2NT-OE TAB-3wk RNA-seq Replicate3

city: Iowa City

first: Long-Sheng

last: Song

state: Iowa

address: 285 Newton Road

department: Department of Internal Medicine

institute: University of Iowa

data_processing:
For raw ChIP-seq and RNA-seq data analyses, the quality control was peformed by FastQC (version 0.11.3) and sequencing adaptors were trimmed by Cutadapt (version 1.8.1).
For ChIP-seq data analyses, processed sequencing reads were aligned to mouse genome (mm10) by Bowtie 2 (version 2.2.5) with the "--end-to--end" mode. MACS (version 1.4.2) with the default parameter was used to call peaks (p value < 10e-10). The Wig format file  (bin size = 10 bp) generated by MACS was normalized by RPM (reads per million) and then converted to bigWig format.
For RNA-seq data analyses, Kallisto (version 0.42.5) with the default parameter was used to quantify gene expression abundance.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq processed data, the bigWig format files were derived from the output of MACS software and normalized by RPM (reads per million, bin size = 10bp). The RNA-seq processed data files were derived from the output of Kallisto with 5 columns splitted by Tab (transcript_id, length, effective_length, estimate_counts and transcrpt per million).

source_name: Left ventricle

growth_protocol: Cardiac specific JP2NT transgene was driven by a-MHC promoter in JP2NT-OE mice. Littermates that don't have the transgene were used as control. Heart samples for JP2NT and TBP ChIP-seq were harveste-d from 2 month old mice. Samples for MEF2C ChIP-seq were from 3 weeks old mice. Heart samples for RNA-seq were harvested from 12 weeks old mice.

extract_protocol:
For ChIP-seq, hearts were excised quickly, rinsed in PBS and snap frozen in liquid nitrogen. ChIP-seq experiments were performed by Active Motif Inc. The samples were crosslinked with PFA, homogenized and sonicated to fragment DNA. The DNA/protein complexes were pulled down by antibodies against  HA tag (Abcam, Catalog #ab9110), TBP (Abcam, Catalog #ab51841) or MEF2C (Santa Cruz, Catalog #sc-313). The crosslinking was reversed and DNA was purified and subjected to library construction. For RNA-seq, the left ventricle tissues were quickly harvested and washed in cold PBS and homogenized in trizol. Trizol manual was followed to extract RNA. Total RNA was treated with DNASE-I (New England Biolabs, Catalog #M0303S) to eliminate genomic DNA and then cleaned using RNA cleanup Kit (Qiagen, Catalog #74204).
For RNA-seq, Illumina TruSeq Stranded mRNA Library Prep Kit (catalog # 20020595) was used to prepare the sequencing library. For ChIP-seq, the sequencing library was prepared by Active Motif, Inc.

treatment_protocol: Transverse aortic banding (TAB) was performed on 9 weeks old male mice. 3 weeks after surgery, hearts were harvested for RNA-seq. Non-treated littermates (no surgery) were used as baseline and harvested on the same time point. For ChIP-seq, all mice were under baseline condition (no TAB surgery).

value: Heart


title: sample_46


title: PB30_MSC_1_BRCA1+/+

description: normal locus

tag: cell type


title: CTCF ChIP DNA, rep1

value: CAST/Ei x 129/Sv/Jae

value: Rabbit anti-CTCF, clone D31H2 (Cell Signaling Technology, #3418)


title: JP2NT-OE TAB-3wk RNA-seq Replicate2


title: CTCF input DNA, rep1


title: sample_989


title: sample_405


title: Control TAB-3wk RNA-seq Replicate3


title: sample_42


title: JP2NT-OE TAB-3wk RNA-seq Replicate1


title: Control TAB-3wk RNA-seq Replicate2


title: sample_41


title: Control TAB-3wk RNA-seq Replicate1


title: JP2NT-OE Baseline RNA-seq Replicate1


title: Control Baseline RNA-seq Replicate2


title: SCNT_KDM6A_Morula_replicate3

city: Yangling

first: Chuan

last: Zhou

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

country: China

institute: Northwest A&F University

description: SCNT embryos

data_processing:
bcl2fastq2 Conversion software (v2.16) was used for basecalling with the parameters bcl2fastq2-v2.16/bin/bcl2fastq --input-dir <runfolder-dir>/Data/Intensities/BaseCalls/ --output-dir <output-dir> --use-bases-mask Y*,Y*,Y*,Y*
Noise reads were removed in raw reads followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 20 is greater than 50% in a read).
The filtered reads were stored in FASTQ format and mapped with HISAT (v0.1.6-beta) to the bovine UMD3.1.1 reference genome with the parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
We used StringTie (v1.0.4) to reconstruct transcripts, and used CuffCompare (v2.2.1) to compare reconstructed transcripts to reference annotation. We then selected  'u','i','o','j' class code types as novel transcripts, and used CPC (v0.9-r2) to predict coding potential of novel transcripts. Complete reference consisted of coding novel   transcripts and reference transcripts.
Clean reads were mapped to the complete reference using Bowtie2 (v2.2.5). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments) using RSEM (v1.2.12).
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript in different samples.

organism: Bos taurus

source_name: SCNT morula embryos

growth_protocol: Ovaries were collected from a local abattoir and transported to the laboratory in sterile saline at 20°C to 25°C within 4 h. Cumulus–oocyte complexes (COCs) collection and in vitro maturation were performed according to the previously described methods in our laboratory. After maturation in vitro for 20-22h, cumulus cells were stripped by vortexing with pipette and oocytes with first polar bodies were selected for the next experiments. Bovine fetal fibroblasts (BFFs) were derived from a female Holstein fetus and cultured in Dulbecco’s Modified Eagle’s Medium containing 10% fetal bovine serum. BFFs were used as donor cells at passage 3-4 and cultivated in low-serum medium (0.5% FBS) for 2 days to induce G0/G1 synchronization. MII oocytes were enucleated in a oil-covered PBS microdrops supplemented with 7.5 ug/mL cytochalasin B and 10% FBS. The first polar body and a few surrounding cytoplasm were aspirated, then the donor cell was injected to subzona of successfully enucleated oocyte. The enucleated oocyte and donor cell was fused with A electrical pulse of 35 V for 10 us in Zimmermann cell fusion medium. After incubation in mSOFaa medium for 2h, cloning embryos were activated in mSOFaa medium containing 5 uM ionomycin for 4 min, then incubated in 2 mM dimethynopyridine for 4 h. Following activation, the SCNT embryos were cultured in mSOFaa until use. Morula embryos were harvested at day 5 after cultured inmSOFaa (day 0).

extract_protocol:
Pools of 5 morula embryos were washed three times in RNase-free PBS solution and transferred into the lysis buffer immediately on ice. Samples were then centrifuged at 10000 rpm for 30 s at 4°C, and stored at -80°C.
Five morula embryos for each sample were directly lysed and used for cDNA synthesis using SuperScript III (Thermo Fisher Scientific). To construct the cDNA library, cDNAs were amplified and fragmented with the NEBNext Ultra DNA Library Prep Kit (E7370, New England Biolabs). Paired-end 150 bp sequencing was performed on the HiSeq4000 (Illumina) platform.

treatment_protocol: The reconstructed embryos were injected with the mRNAs encoding wild-type KDM6A of bos taurus at 1 h after activation. After cultured for five days, the morula embryos were selected for RNA-seq. The cloned morula without injecting regard as control.

tag: breed

value: Holstein

tag: developmental stage

value: morula

value: KDM6A overexpression


title: SCNT_Morula_replicate3

description: SCNT embryos

value: control


title: JP2NT-OE Baseline RNA-seq Replicate3


title: SCNT_8C_replicate1

description: SCNT embryos

source_name: SCNT eight-cell embryos

value: eight-cell embryos


title: RBPJ-KO_K+I+Treg_R3

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

data_processing:
For all samples, low quality bases were removed with Fastq_quality_filter from the FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) with 90 percent of the read needing a quality phred score > 20. Homertools 4.756 were used for PolyA-tail trimming, and reads with a length < 17 were removed. PicardTools 1.78 (https://broadinstitute.github.io/picard/) were used to compute the quality metrics with CollectRNASeqMetrics. With STAR 2.357, the filtered reads were mapped against mouse genome 38 using default parameters. Count data and RPKM tables were generated by mapping filtered reads against union transcripts (derived from Mouse Ensembl 90) using a custom pipeline. Mapping was carried out with bowtie2 version 2.2.458 against union mouse genes: every gene is represented by a union of all its transcripts (exons). The count values (RPKM and raw counts) were calculated by running CoverageBed from Bedtools v2.26.059 of the mapped reads together with the mouse annotation file (Ensembl 90) in gtf format and parsing the output with custom perl scripts. The input tables containing the replicates for groups to compare were created by a custom perl script. For DESeq2, DESeqDataSetFromMatrix was applied, followed by estimateSizeFactors, estimateDispersions, and nbinomWald testing. The result tables were annotated with gene information (gene symbol, gene type) derived from the gencode.vM16.annotation.gtf file. The results were then filtered for protein-coding genes according to the gencode.vM16.annotation.gtf file. To account for the gender differences between male and female mice, 4571 differently expressed genes with an adj. P-value < 0.05 in the comparison of wildtype spleen-derived TCRβ+CD4+CD8-CD25+Foxp3(GFP)+Klrg1-ST2- (female) with wildtype spleen-derived TCRβ+CD4+CD8-CD25+Foxp3(GFP)+Klrg1-ST2- (male) cells were excluded from the input tables into DESeq2 and the analyses were rerun with the remaining genes. MA plots were generated as described (reference see original publication). PCA plots and tables were generated using the plotPCA function of DESeq2 for the most variable 500 genes after applying the DESeq2 varianceStabilizingTransformation to the data.
Genome_build: mm10

source_name: Rbpj KO

extract_protocol:
Spleen was isolated and target cells were sorted using FACS; RNA was isolated with the RNEasy Mini Kit
cDNA was generated and amplified using 4.8 ng of total RNA (RNEeasy Mini Kit) and SMARTer Ultra Low Input RNA for Illumina Sequencing - HV (Clontech Laboratories, Inc.) according to the manufacturer’s protocol. Then, sequencing libraries were prepared using the NEXT ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs) according to the manufacturer's instructions with the following modifications: The adapter-ligated double-stranded cDNA (10µl) was amplified using NEBNext Multiplex Oligos for Illumina (New England Biolabs, 25 µM primers), NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) and 15 cycles of PCR. Final libraries were validated using Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit flourometer (Invitrogen), normalized and pooled in equimolar ratios. 50bp single-read sequencing was performed on the Illumina HiSeq 2000 v4 according to the manufacturer’s protocol.

treatment_protocol: Mice were housed at DKFZ central animal facility and analyzed upon signs of disease

tag: organ

value: Spleen

value: CD4+CD25+Foxp3(GFP)+ Treg

tag: cell subtype

value: Klrg1-positive ST2-positive


title: Control Baseline RNA-seq Replicate3


title: SCNT_KDM6A_Morula_replicate2

description: SCNT embryos


title: RBPJ-KO_K+I+Treg_R1


title: SCNT_KDM6A_Morula_replicate1

description: SCNT embryos


title: RBPJ-KO_K+I+Treg_R2


title: SCNT_8C_replicate2

description: SCNT embryos


title: SCNT_Morula_replicate1

description: SCNT embryos


title: SCNT_Morula_replicate2

description: SCNT embryos


title: RBPJ-KO_K-I-Treg_R2

value: Klrg1-negative ST2-negative


title: RBPJ-KO_K-I-Treg_R1


title: SCNT_8C_replicate3

description: SCNT embryos


title: MK2

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Transcripts for R26 tdTomato were added to the mm10 genome.
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices.
Celllranger datasets consist of (for each sample) matrix files (matrix.mtx) containing the UMI count values, barcode files (barcodes.tsv) containing the detected cell barcodes and genes files (genes.tsv)  containing the ENSEMBL ids of the detected genes.  The first 26 bp of R1 reads contain the barcode (16bp) and UMI (10bp) respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files, compressed.

source_name: E15.5 embryonic kidneys

extract_protocol:
E15.5 embryonic kidneys were dissected and dissociated in 1mg/ml liberase (Roche) on ice for 25 minutes. Samples were gently agitated by pipetting every 5 minutes. Samples were filtered, washed once with cold PBS and pelleted by centrifugation. Samples were resuspended at the appropriate concentration and stored on ice prior to the generation of single cell libraries using the 10X platform.
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

treatment_protocol: Pregnant females were treated with 2mg Tamoxifen IP at E10.5, E11.5, E12.5 and E13.5 to induce tdTomato labelling of Wnt4 expressing cells in embryos.

value: embryonic kidneys


title: MK3


title: 254890810729_2_4: D2 chronic (cured) acute vs. D2 chronic (cured)

description:
(-) polarity
254890810729_2_4

value: fallopial tube

tag: donor

value: organoid donor 2

value: chronic (cured) acute

source_name: D2 Ctr infection - cured

value: chronic (cured)


title: RBPJ-WT_K-I-Treg_R3

source_name: Rbpj WT


title: Gene expression 4 hours after heme induction_∆hrrA

city: Juelich

first: Andrei

last: Filipchyk

address: Wilhelm-Johnen-Straße

institute: FZ-Juelich

data_processing:
Reads quality was checked with FASTQC. No trimming was undertaken
Identical reads were collapsed into single records using custom script
Reads were mapped to C. glutamicum genome with Bowtie2. Bowtie2 was ran with the following parameters: bowtie2 -1 [path to the reads, 1st mate] -2 [path to the reads, 2nd mate] -S [path to the mappings] –phred33 –sensitive-local –local –score-min C,90 –rdg 9,5 –rfg 9,5 -a –no-unal -I 40 -X 400 –no-mixed –ignore-quals
Transcript per million values were estimated for the C. glutamicum genes annotated in Baumgart et al., ACS synthetic biology, 2018
Genome_build: BX927147
Supplementary_files_format_and_content: Processed data are in tab separated format. 1st column is gene name, 2nd – expression (in transcripts per million) for the wild type replicates (divided by ‘;’ ), 3rd  – expression (in transcripts per million) for the hRRA KO replicates (divided by ‘;’ )

organism: Corynebacterium glutamicum ATCC 13032

source_name: ∆hrrA_4h after heme induction

growth_protocol: A preculture was inoculated in liquid BHI medium (25 µg/ml kanamycin) from a fresh BHI agar plate and incubated for 8-10 h at 30°C in a rotary shaker. After that, cells were transferred into a second preculture in CGXII medium containing 2 % (w/v) glucose and 0 µM FeSO4 to starve the cells from iron protocatechuic acid (PCA), which was added to the medium, allowed the uptake of trace amounts of iron. From an overnight culture, the main cultures were inoculated (CGXII medium containing 4µM heme) and harvested 0h, 0.5h or 4h after inoculation

extract_protocol:
RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany), ribosomal RNA was removed by running twice the workflow of the Ribo-Zero rRNA Removal Kit (Illumina, California, USA)
after fragmentation of RNA, cDNA strand synthesis and indexing was carried out using the TruSeq® Stranded mRNA Library Prep Kit (Illumina, California, USA) according to the supplier’s manual.

treatment_protocol: For the preparation of the RNA, the pellets were resuspended in RTL bufferand the cells disrupted by 3x30 sec silica bead beating, 6000 rt/min. After ultra-centrifugation (150.000xg, 4 °C, 1 h), the RNA was purified using the RNeasy Mini Kit

value: {delta}hrrA

tag: medium

value: CGXII

tag: heme concentration

tag: time point

tag: molecule subtype

value: Total RNA (Ribo-minus)


title: MK1


title: Gene expression 4 hours after heme induction_WT

source_name: WT_4h after heme induction

value: wild type


title: JP2NT-OE Baseline RNA-seq Replicate2

value: Heart


title: RBPJ-KO_K-I-Treg_R3


title: RBPJ-WT_K-I-Treg_R1


title: Control Baseline RNA-seq Replicate1


title: Gene expression 0.5 hours after heme induction_∆hrrA

source_name: ∆hrrA_0.5h after heme induction


title: Gene expression 0.5 hours after heme induction_WT

source_name: WT_0.5h after heme induction


title: Fmr1-KO rep1

city: Madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned to the mouse genome GRCm38 with annotation from Gencode (gencode.vM15.primary_assembly.annotation.gtf)using STAR (v2.5.3a) with options: --runMode alignReads --clip3pAdapterSeq AGATCGGAAG --outSAMunmapped None --outFilterMultimapNmax 5 --outFilterMultimapScoreRange 1 --outFilterMismatchNoverLmax 0.06 --alignIntronMin 20 --alignIntronMax 1000000 -alignSJDBoverhangMin 1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 5000000000 --quantMode GeneCounts _ --outSAMattributes All --outFilterType BySJout --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd
Reads mapped to the “+” strand of annotated genes were counted by STAR using the above option “--quantMode GeneCounts”
EBSeq (v1.18.0) was used to test for differential expression in two WT and KO samples and differentially expressed genes were defined using a cutoff of PPEE<0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel files include reads count of genes
Supplementary_files_format_and_content: bigwig files of read coverage

source_name: DG

extract_protocol:
DG tissue were isolated from 6-7 weeks old Fmr1-/y; Dcx-DsRed mice and their WT littermates. All cell populations were isolated into single cells using a Becton Dickinson FACS Aria II contained in a Biosafety Carbinet using 20 psi pressure and 100-μm nozzle aperture. 10,000 total alive or Dcx-DsRed+ alive Cells were collected directly in Trizol. Total RNA from the sorted cell was isolated using the Direct-zol™ RNA MiniPrep Kit.
Strand-specific, poly(A) selected cDNA libraries were generated using Nugen  Ovation® Ultralow Library Systems  (Illumina) according to the manufacturer’s protocol.  Cluster generation and high-throughput sequencing were performed on a HiSeq 2500 (Illumina), using the paired-end 100 bp protocol. Reads were aligned to the mouse genome GRCm38 with annotation from Gencode.

value: DG

tag: age

value: 6-7 weeks old


title: Gene expression Before heme induction_∆hrrA_

source_name: ∆hrrA_before heme induction


title: WT rep1

tag: strain


title: RBPJ-WT_K-I-Treg_R2


title: Spleen K- Treg R2


title: Fmr1-KO rep2


title: Spleen K- Treg R1


title: WT rep2


title: C57Bl6_Thiomac_RNA_Veh_VML_15-02-17

city: La Jolla

first: Jenhan

last: Tao

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Reads from each RNA-Seq sample were aligned to the mm10 genome using STAR.
Aligned read files were analyzed with HOMER (http://homer.ucsd.edu/homer/) to calculate RPKM from the exons of RefSeq genes (using the following command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -rpkm)
BigWig tracks were created using the HOMER makeBigWig.pl command
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include a expression text file that contains expression values for each sample (RNA-Seq expression data, using the following HOMER command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -rpkm).  All genomic coordinates are relative to mm10 human assembly.

source_name: mouse thioglycollate elicited macrophage cells

growth_protocol: TGEMs were grown for 3 days in 10%FBS, 1%Penicillin Streptomycin, DMEM

extract_protocol:
RNA isolation. RNA was isolated using TRIZOL-reagent (ambion cat# 15596018) and DIRECT-ZOL RNA mini-prep kit (cat# 11-330MB). Poly-A RNA isolation. Use 0.2 Total RNA as starting material for ideal mapping efficiency and minimal clonality.  Collect 10 μL oligo (dT) (NEB cat# S1419S) beads per RNA sample. Beads were washed twice with 1x DTBB (20mM Tris-HCl pH7.5, 1M LiCl, 2mM EDTA, 1% LDS, 0.1% Triton X-100). Beads were resuspended in 50uL of 2x DTBB.  50uL of beads were mixed with 50uL RNA and Heated to 65°C for 2 min. RNA-beads were then incubated for 10 min at RT while rotating. RNA-beads were then collected on a magnet and washed 1x each with RNA WB1 (10mM Tris-HCl pH7.5, 0.12 M LiCl, 1mM EDTA, 0.1% LDS, 0.1% Triton X-100)and WB3 (10mM Tris-HCl pH7.5, 0.5M LiCl, 1mM EDTA). Add 50uL Tris-HCl pH7.5 and heat to  80°C for 2 min to elute. Collect RNA and perform a second Oligo-dT bead collection. After washing the second collection, instead of eluting was 1X with 1X First strand buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2 [ThermoFisher SSIII kit Cat# 18080093). Fragmentation. Then Add 10uL of 2X First strand buffer plus 10mM DTT and fragment DNA at 94°C for 9 min. Collect beads on magnet and transfer eluate containing fragmented mRNA to a new PCR strip.  Should recover 10 μL fragmented RNA. First strand synthesis. We mixed fragmented RNA with 0.5uL Random Primer (3 μg/μL) Life Tech #48190-011, 0.5uL oligo-dT (50uM from SSIII kit), 1uL dNTPs (10mM Life Tech, cat 18427088) and 0.5uL SUPERase-In (ThermoFisher Cat#AM2696) and heat 50°C for 1 min. Immediately place on ice. We then added 5.8uL ddH2O, 0.1 uL Actinomycin (2ug/uL Sigma cat#A1410), 1uL DTT (100mM Life Tech cat# P2325), 0.2uL of 1% Tween and 0.5 uL of Superscript III and incubate 25°C for 10 min, then 50°C for 50 min. Bead clean up. We added 36 μL of RNAClean XP (ampure XP) and mixed, incubating for 15 min on ice. The beads were then collected on a magnet and washed 2X with 75% ethanol. Beads were then air-dried for 10 min and elute with 10 μL nuclease free H2O. Second strand synthesis. 10uL of cDNA/RNA was mixed with 1.5uL 10X Blue Buffer (Enzymatics cat# B0110L), 1uL dUTP/dNTP mix (10mM Affymatrix cat# 77330), 0.1uL dUTP (100mM Affymatrix cat# 77206), 0.2uL RNase H (5U/uL Enzymatics cat# Y9220L), 1uL DNA polymerase I (10U/uL Enzymatics cat#P7050L), 0.15 uL 1% Tween-20 and 1.05uL nuclease free water. Reaction was incubated at 16°C for 2.5 hours. Bead clean up. DNA was purified by adding 1uL Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) per reaction in 28uL 20% PEG8000/2.5 M NaCl (13% final concentration) and incubating at RT for 10min. Beads were then collected on a magnet and washed 2X with 80% Ethanol. Beads were air-dried for 10min and eluted in 40uL of nuclease free water. DNA is ready for library prep.
dsDNA End Repair. We mixed 40uL of DNA from ChIP or RNA protocols with 2.9uL of H2O, 0.5uL 1% Tween-20, 5uL 10X T4 ligase buffer (Enzymatics cat# L6030-HC-L), 1uL dNTP mix (10 mM  Affymetrix 77119), 0.3 uL T4 DNA pol (Enzymatics P7080L), 0.3uL T4 PNK (Enzymatics Y9040L), 0.06uL Klenow (Enzymatics P7060L) and incubated for 30min at 20°C. 1uL of Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) in 93 μL 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Bead clean-up. Beads were collected on a magnet and washed 2X with 80% ethanol. Beads were air-dried for 10 min and then eluted in 15uL ddH2O. dA-Tailing. DNA was mixed with 10.8uL ddH2O, 0.3uL 1% Tween-20, 3uL Blue Buffer (Enzymatics cat# B0110L), 0.6uL dATP (10mM Tech 10216-018), 0.3uL Klenow 3’- 5’ Exo (Enzymatics P7010-LC-L) and incubated for 30min at 37°C. 55.8uL 20% PEG8000/2.5 M NaCl (13% final) was added an incubated for 10 min. Then bead clean up was done. Beads were eluted in 14uL. Y-Shape Adapter Ligation. Sample was mixed with 0.5uL of a BIOO barcode adapter (BIOO Scientific cat# 514104), 15uL Rapid Ligation Buffer (Enzymatics cat@ L603-LC-L), 0.33uL 1% Tween-20 and 0.5uL T4 DNA ligase  HC (Enzymatics L6030-HC-L) and incubated for 15 min at RT.  7 μL of 20% PEG8000/2.5 M NaCl was added and incubated for 10min at RT. Bead clean up was performed and beads were eluted in 21uL. 10uL was then used for PCR amplification (14 cycles) with IGA and IGB primers (AATGATACGGCGACCACCGA, CAAGCAGAAGACGGCATACGA).

treatment_protocol: Veh (PBS) or KLA were added directly to the media

value: male

tag: treatment

value: Vehicle


title: Spleen K- Treg R4

value: Spleen

value: CD4+CD25+Foxp3(GFP)+ Treg


title: Spleen tisTreg2 R3

value: Klrg1-positive ST2-positive


title: Spleen K- Treg R3

value: Klrg1-negative ST2-negative


title: Spleen tisTreg2 R2


title: Balbc_Thiomac_RNA_KLA-1h_VML_15-02-26

value: mouse thioglycollate elicited macrophage cells

value: KLA 1h

value: Balb/cJ


title: Balbc_Thiomac_RNA_Veh_VML_14-12-01


title: CUP patient 137

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

institute: Kinki university School of Medicine

hyb_protocol: IVT products were magnetic-bead purified, frangmented, and hybridized onto Affymetrix U133 plus 2.0 GeneChip at 45° C for 16 h.

scan_protocol: Scanner in an Affymetrix GeneChip Scanner 3000 7G (Santa Clara, CA).

data_processing: Data extraction was done by the Affymetrix GCOS software v1.4.

source_name: metastatic lesion

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

extract_protocol: The mRNA extraction was done using the Isogen protocol

value: lymph node

tag: disease state

value: cancer of unknown primary


title: Spleen tisTreg2 R4


title: Balbc_Thiomac_RNA_KLA-1h_VML_14-12-01

tag: genotype


title: CUP patient 136

tag: tissue


title: CUP patient 135


title: CUP patient 133


title: CUP patient 132


title: C57Bl6_Thiomac_ChIP_PU1_KLA-1h

data_processing:
Reads from each ChIP-seq sample were aligned to the mm10 build of the mouse genome using bowtie2 (with default parameters).
Sam files were converted to tag directories with HOMER
Peaks were called with HOMER with the findPeaks command using the corresponding input file and the parameters -L 0 -C 0 -fdr 0.9
HOMER peak scores from peak files corresponding to replicate experiments were used as input for IDR; peaks with IDR < 0.05 were retained
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file giving the genomic coordinates of putative binding site for each ChIP target. The "count" column indicates the HOMER peak score

extract_protocol:
Protein A and G Dynabeads 50/50 mix from Invitrogen are sued for ChIP (10001D, 10003D). IP mix consists of 20ul beads/2ug antibody per 2 million cell ChIP. For preparation, beads were washed with 0.5%BSA-PBS (BSA: , then incubate beads-antibody with 0.5%BSA-PBS for at least 1h on rotator (4oC). Wash 2X with 0.5%BSA-PBS, then resuspend in dilution buffer. Double Crosslinking for ChIP. Media was decanted from cells in 10 cm plates, wash once briefly with PBS (RT). Disuccinimidyl glutarate (Pierce Cat # 20593)  (diluted in DMSO at 200mM)/PBS (RT) was used for 10 min. Then Formaldehyde was added to a final concentration of 1% for an additional 10 min. Reaction was quenched with 1:10 Tris pH 7.4 on ice. Cells were collected and washed twice with cold PBS, spinning at 1000 rcf for 5 min. Nuclei Isolation and Sonication. Resuspend cell pellets in 1 ml of Nuclei Isolation Buffer (50 mM Tris-Ph 8.0, 60 mM KCl, 0.5% NP40) + PI and incubate on ice for 10 minutes. Centrifuge 2,000 g for 3 minutes at 4º C. Resuspend nuclei in 200 ul of fresh Lysis Buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (ph8))+ PI. Sonication. Nuclei were then sonicated (10 million cells) for 25 minutes in a Biorupter (settings= 30 seconds=On, 30 seconds=Off, Medium) using thin wall tubes (Diagenode Cat# C30010010). After sonication spin max speed for 10 minute at 4C.  ChIP set up. Sonicated DNA was diluted 5X with 800 Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (ph8), 1X Protease Inhibitors).  An aliquot is removed for input samples (5%).  Samples ON at 4º C while rotating. Washing. ChIP are washed 1X with TSE I (20mM Tris-HCl pH7.4, 150mM NaCl, 0.1%SDS, 1% Triton X-100, 2mM EDTA), 2X with TSE III (10mM Tris-HCl pH7.4, 250mM LiCl, 1%IGEPAL, 1%Deoxycholate, 1mM EDTA), 1X with TE+0.1%TritonX-100, transfer to new tube and then wash another time with TE+0.1%TritonX-100.   Elution. Elute with 200 uL Elution Buffer (1% SDS, 10mM Tris pH7.5) for 20 minutes at RT, shaking on the vortex or a nutator or rotator.  De-crosslinking. Add 10 uL of 5 M NaCl and incubate ON at 65º C (or at least 8 hours).  Clean up samples using Zymo ChIP DNA Clean & Concentrator. Elute in 100uL. Take 40uL and proceed to library prep protocol.
dsDNA End Repair. We mixed 40uL of DNA from ChIP or RNA protocols with 2.9uL of H2O, 0.5uL 1% Tween-20, 5uL 10X T4 ligase buffer (Enzymatics cat# L6030-HC-L), 1uL dNTP mix (10 mM  Affymetrix 77119), 0.3 uL T4 DNA pol (Enzymatics P7080L), 0.3uL T4 PNK (Enzymatics Y9040L), 0.06uL Klenow (Enzymatics P7060L) and incubated for 30min at 20°C. 1uL of Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) in 93 μL 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Bead clean-up. Beads were collected on a magnet and washed 2X with 80% ethanol. Beads were air-dried for 10 min and then eluted in 15uL ddH2O. dA-Tailing. DNA was mixed with 10.8uL ddH2O, 0.3uL 1% Tween-20, 3uL Blue Buffer (Enzymatics cat# B0110L), 0.6uL dATP (10mM Tech 10216-018), 0.3uL Klenow 3’- 5’ Exo (Enzymatics P7010-LC-L) and incubated for 30min at 37°C. 55.8uL 20% PEG8000/2.5 M NaCl (13% final) was added an incubated for 10 min. Then bead clean up was done. Beads were eluted in 14uL. Y-Shape Adapter Ligation. Sample was mixed with 0.5uL of a BIOO barcode adapter (BIOO Scientific cat# 514104), 15uL Rapid Ligation Buffer (Enzymatics cat@ L603-LC-L), 0.33uL 1% Tween-20 and 0.5uL T4 DNA ligase  HC (Enzymatics L6030-HC-L) and incubated for 15 min at RT.  7 μL of 20% PEG8000/2.5 M NaCl was added and incubated for 10min at RT. Bead clean up was performed and beads were eluted in 21uL. 10uL was then used for PCR amplification (14 cycles) with IGA and IGB primers (AATGATACGGCGACCACCGA, CAAGCAGAAGACGGCATACGA).

tag: Sex

tag: antigen target

tag: library prep

value: ChIP


title: CUP patient 134


title: Spleen tisTreg2 R1

tag: cell type


title: C57Bl6_Thiomac_ChIP_Fra2_Veh

value: Veh


title: C57Bl6_Thiomac_ChIP_JunB_KLA-1h

value: JunB (sc-73)


title: CUP patient 131


title: C57Bl6_Thiomac_ChIP_Fos_Veh


title: C57Bl6_Thiomac_ChIP_Fos_KLA-1h


title: Gene expression Before heme induction_WT

source_name: WT_before heme induction

tag: genotype/variation

value: wild type

value: CGXII

value: Total RNA (Ribo-minus)


title: C57Bl6_Thiomac_ChIP_PPARg_Veh

value: male


title: C57Bl6_Thiomac_RNA_KLA-1h_VML_15-02-17


title: CUP patient 130


title: CUP patient 129


title: CUP patient 127


title: CUP patient 128


title: CUP patient 126


title: CUP patient 124


title: CUP patient 123


title: Organoid Neurog3Chrono positive single cell transcriptomes 7

city: Utrecht

first: Helmuth

last: Gehart

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
sorted Neurog3Chrono-positive cells from murine small intestinal organoids
CEL-Seq2_UMI_singleCell_barcodes_384.csv

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 (96 primer method) or 6 bases (384 primer method) 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: murine small intestinal organoids

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Live cells positive for Neurog3Chrono 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 (96 primer method) or 6bp (384 primer method) 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: Neurog3Chrono hom

value: intestine

value: sorted Neurog3Chrono-positive cells

tag: method

value: CEL-Seq2 384 primer


title: Organoid Neurog3Chrono positive single cell transcriptomes 6


title: CUP patient 117


title: CUP patient 115


title: CUP patient 114


title: Organoid Neurog3Chrono positive single cell transcriptomes 5


title: Organoid Neurog3Chrono positive single cell transcriptomes 4


title: CUP patient 122


title: CUP patient 119


title: CUP patient 125


title: CUP patient 120


title: CUP patient 118


title: CUP patient 121


title: CUP patient 108

value: ascites/hydrothorax


title: CUP patient 109


title: CUP patient 113


title: CUP patient 116


title: CUP patient 112


title: CUP patient 107


title: CUP patient 103


title: CUP patient 110


title: CUP patient 104


title: Organoid Neurog3Chrono positive single cell transcriptomes 3


title: Organoid Neurog3Chrono positive single cell transcriptomes 2


title: Intestinal Neurog3Chrono positive single cell transcriptomes 14

description:
sorted Neurog3Chrono-positive cells from murine small intestine
CEL-Seq2_UMI_singleCell_barcodes_384.csv

source_name: murine small intestinal epithelium


title: Intestinal Neurog3Chrono positive single cell transcriptomes 18


title: Intestinal Neurog3Chrono positive single cell transcriptomes 17


title: CUP patient 106


title: Intestinal Neurog3Chrono positive single cell transcriptomes 16


title: CUP patient 111


title: Intestinal Neurog3Chrono positive single cell transcriptomes 15


title: CUP patient 105


title: CUP patient 101


title: CUP patient 102


title: Organoid Neurog3Chrono positive single cell transcriptomes 1


title: Intestinal Neurog3Chrono positive single cell transcriptomes 12


title: Intestinal Neurog3Chrono positive single cell transcriptomes 11


title: Intestinal Neurog3Chrono positive single cell transcriptomes 10


title: Intestinal Neurog3Chrono positive single cell transcriptomes 9


title: Intestinal Neurog3Chrono positive single cell transcriptomes 6


title: Intestinal Neurog3Chrono positive single cell transcriptomes 13


title: Intestinal Neurog3Chrono positive single cell transcriptomes 8


title: Intestinal Neurog3Chrono positive single cell transcriptomes 5


title: Intestinal Neurog3Chrono positive single cell transcriptomes 4


title: CUP patient 95


title: Intestinal Neurog3Chrono positive single cell transcriptomes 3


title: CUP patient 99


title: CUP patient 100


title: CUP patient 96


title: Intestinal Neurog3Chrono positive single cell transcriptomes 2d

description:
sorted Neurog3Chrono-positive cells from murine small intestine
CEL-Seq_UMI_singleCell_barcodes_96.csv

value: CEL-Seq 96 primer


title: CUP patient 97


title: CUP patient 98


title: CUP patient 94


title: Intestinal Neurog3Chrono positive single cell transcriptomes 7


title: CUP patient 92


title: Intestinal Neurog3Chrono positive single cell transcriptomes 2b


title: Intestinal Neurog3Chrono positive single cell transcriptomes 2a


title: CUP patient 93


title: Intestinal Neurog3Chrono positive single cell transcriptomes 1d


title: CUP patient 83


title: CUP patient 87


title: CUP patient 88


title: Intestinal Neurog3Chrono positive single cell transcriptomes 1c


title: Intestinal Neurog3Chrono positive single cell transcriptomes 1b


title: CUP patient 91

description: patients #89 & 90 ineligible.


title: CUP patient 82


title: Intestinal Neurog3Chrono positive single cell transcriptomes 2c


title: CUP patient 85


title: Intestinal Neurog3Chrono positive single cell transcriptomes 1a


title: CUP patient 86


title: D15_serum_GDF9_ctrl_1.0_C1 (bulk RNA-seq)

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Reads were aligned to the UCSC mm10 transcriptome (using RNA-Seq genome-aligner  STAR), and a matrix of UMI counts was obtained using CELLRANGER from the 10X Genomics pipeline  (v2.0.0) with default parameters. Bulk RNAseq data were analyzed as follows: reads (83 bp) were aligned to the UCSC mm10 transcriptome, and a matrix of read counts was obtained using the QuantSeq processing pipeline (http://rpubs.com/chapmandu2/171024) with the reference genome sequence and gene annotations (GTF file) from the Cellranger 10X Genomics pipeline (v2.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation).
Genome_build: mm10
Supplementary_files_format_and_content: expression_matrix_GDF9_bulk.csv.gz, h5

source_name: 2nd MEFs

growth_protocol: To determine the effect of GDF9 on reprogramming, we plated secondary MEFs at a concentration of 5,000 cells per well of a 24-well plate and added either recombinant mouse GDF9 (R&D Systems, 739-G9-010, lot SOZ0516121) daily from day 8 onward, or control (0.1% Bovine Serum Albumin in 4 mM HCl, R&D Systems, RB04). We initially tested different doses (0, 0.1 µg/ml, 0.5 µg/ml, and 1 µg/ml) and then confirmed results seen at the highest dose in multiple independent experiments. We used three distinct approaches to determine the proportion of pluripotent cell at day 15: (i) counting the number of Oct4-EGFP+ colonies using a fluorescence microscope, (ii) bulk RNAseq (Quantseq, Lexogen) and (iii) scRNAseq. For each assay, experiments were performed in biological triplicates (each assay using separate replicates).

extract_protocol:
We collected a total of ~50,000 cells. For all collections, selected wells were trypsinized for 5 mins followed by inactivation of trypsin by addition of MEF medium. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3’ Reagent Kits v2  according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry. Bulk RNA-seq libraries were generated from QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Libraries were made according to manufacturer's protocol and sequenced on illumina NextSeq 500.

value: 2nd MEFs (OKSM)

tag: agent

value: control

tag: time

value: day 15


title: CUP patient 81

value: lymph node

value: cancer of unknown primary


title: CUP patient 79


title: CUP patient 84


title: D15_serum_GDF9_ctrl_0.5_C3 (bulk RNA-seq)


title: D15_serum_GDF9_ctrl_1.0_C2 (bulk RNA-seq)


title: CUP patient 80


title: D15_serum_GDF9_ctrl_0.5_C2 (bulk RNA-seq)


title: D15_serum_GDF9_ctrl_1.0_C3 (bulk RNA-seq)


title: D15_serum_GDF9_ctrl_0.5_C1 (bulk RNA-seq)


title: CUP patient 78

description: patient #77 ineligible.


title: D15_serum_GDF9_ctrl_0.1_C1 (bulk RNA-seq)


title: D15_serum_GDF9_ctrl_0.1_C2 (bulk RNA-seq)


title: CUP patient 73


title: CUP patient 72


title: CUP patient 69


title: CUP patient 68


title: D15_serum_GDF9_exp_1.0_C2 (bulk RNA-seq)

tag: dose

value: 1.0 µg/ml


title: D15_serum_GDF9_exp_1.0_C3 (bulk RNA-seq)


title: CUP patient 71


title: CUP patient 63


title: CUP patient 65


title: D15_serum_GDF9_exp_1.0_C1 (bulk RNA-seq)


title: CUP patient 70


title: CUP patient 76


title: CUP patient 62


title: CUP patient 74


title: CUP patient 67


title: CUP patient 75


title: CUP patient 64


title: CUP patient 66


title: D15_serum_GDF9_exp_0.5_C2 (bulk RNA-seq)

value: 0.5 µg/ml


title: D15_serum_GDF9_exp_0.5_C3 (bulk RNA-seq)


title: D15_serum_GDF9_exp_0.5_C1 (bulk RNA-seq)


title: D15_serum_GDF9_exp_0.1_C3 (bulk RNA-seq)

value: 0.1 µg/ml


title: D15_serum_GDF9_exp_0.1_C2 (bulk RNA-seq)


title: D15_serum_GDF9_exp_0.1_C1 (bulk RNA-seq)


title: D15_serum_GDF9_ctrl_R4_C3 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R4_C2 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R3_C3 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R4_C1 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R3_C2 (scRNA-seq)


title: CONTROL 0hr replicate 4

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, axolotl embryo tail tip tissue. Samples were untreated and collected at the time of amputation

hyb_protocol: Microarray hybridization using an Ambystoma Affymetrix array (Huggins et al., 2012) was performed by the University of Kentucky Microarray Core Facility.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing: Day 0 normalized values are not present because they were not used for statistical analyses.  However, we provide the raw CEL files for individuals who are interested in the analysis.

organism: Ambystoma mexicanum

source_name: 1.0mm distal tip of amputated axolotl embryo tails, at time of amputation. Samples were untreated.

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: The use of pre-feeding stage axolotls does not require a protocol approved by the Institutional Animal Care and Use Committee (IACUC) at University of Kentucky, however embryos used in this study were treated according to the same ethical standards that apply to feeding axolotls. Rearing water (40% modified Holtfretter's solution) was changed three times per week.

extract_protocol: The tissue samples were maintained at 4 C in RNA later prior to RNA isolation using first the Trizol method and then a Qiagen minikit with on-the-column DNAse treatment of DNA.

treatment_protocol: Developmental stage 42 (Bordzilovskaya et al 1989) axolotl embryos were manually hatched by removing the egg jelly and membrane, anesthetized in 0.02% benzocaine, and administered tail amputations with a razor blade to remove 2 mm (~20% of the body length) of the distal tail tip. After amputation, animals were placed into microtiter plates containing rearing water (40% modified Holtfreter’s Solution) and 0.001% DMSO (controls) or rearing water with 10 um romidepsin or 10 um belinostat (treatements).

tag: time (hpa)

value: Control


title: D15_serum_GDF9_ctrl_R2_C3 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R2_C2 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R2_C1 (scRNA-seq)


title: CONTROL 0hr replicate 2


title: SU090 GMP

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

institute: UCSD

description: SU090 GMP, Elderly, Anemia of unexplained etiology

hyb_protocol: Fifteen micrograms of cRNA from each sample was hybridized to Affymetrix HG U133 Plus 2.0 microarrays. Hybridization was performed according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Scanning was performed according to the manufacturer’s instructions (Affymetrix).

data_processing: RMA log2 expression values computed using libaffy-2.1.5/bin/iron --norm-quantile --median-polish

source_name: Human Bone Marrow GMP, Elderly, Anemia of unexplained etiology

label_protocol: All RNA samples were quantified with the RiboGreen RNA Quantitation Kit (Molecular Probes), subjected to re- verse transcription, two consecutive rounds of linear amplification, and production and fragmentation of biotinylated cRNA (Affymetrix).

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) or Ambion RNA Isolation Kit (Applied Biosystems by Life Technologies) according to the manufacturer’s protocols and treated with DNase I (Qiagen).

treatment_protocol: Untreated

tag: immunophenotype

value: GMP


title: SU090 MEP

description: SU090 MEP, Elderly, Anemia of unexplained etiology

source_name: Human Bone Marrow MEP, Elderly, Anemia of unexplained etiology

value: MEP


title: SU102 CMP

description: SU102 CMP, Elderly, Anemia of unexplained etiology

source_name: Human Bone Marrow CMP, Elderly, Anemia of unexplained etiology

value: CMP


title: SU117 HSC

description: SU117 HSC, Elderly, Anemia of unexplained etiology

source_name: Human Bone Marrow HSC, Elderly, Anemia of unexplained etiology

value: HSC


title: D15_serum_GDF9_ctrl_R1_C3 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R1_C2 (scRNA-seq)


title: SU060 HSC

description: SU060 HSC, Elderly, Anemia of unexplained etiology


title: SU102 MEP

description: SU102 MEP, Elderly, Anemia of unexplained etiology


title: SU117 GMP

description: SU117 GMP, Elderly, Anemia of unexplained etiology


title: SU090 CMP

description: SU090 CMP, Elderly, Anemia of unexplained etiology


title: SU060 MEP

description: SU060 MEP, Elderly, Anemia of unexplained etiology


title: SU060 CMP

description: SU060 CMP, Elderly, Anemia of unexplained etiology


title: SU090 HSC

description: SU090 HSC, Elderly, Anemia of unexplained etiology


title: SU102 HSC

description: SU102 HSC, Elderly, Anemia of unexplained etiology


title: D15_serum_GDF9_ctrl_R3_C1 (scRNA-seq)


title: D15_serum_GDF9_ctrl_R1_C1 (scRNA-seq)


title: SU117 MEP

description: SU117 MEP, Elderly, Anemia of unexplained etiology


title: CONTROL 0hr replicate 3


title: D15_serum_GDF9_exp_R4_C3 (scRNA-seq)


title: D15_serum_GDF9_exp_R4_C2 (scRNA-seq)


title: D15_serum_GDF9_exp_R4_C1 (scRNA-seq)


title: SU102 GMP

description: SU102 GMP, Elderly, Anemia of unexplained etiology


title: D15_serum_GDF9_exp_R3_C3 (scRNA-seq)


title: SU117 CMP

description: SU117 CMP, Elderly, Anemia of unexplained etiology


title: CONTROL 6hr replicate 3

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected 6 hours post amputation.

data_processing: GeneChips were normalized using the affy R package (Gautier et al 2004) Affymetrix Expression Console software to accomplish robust multichip averaging (RMA) (Irizarry et al., 2003).

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails, at 6 hpa. Samples were untreated.


title: ROMIDEPSIN 6hr replicate 1

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 6 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails, at 6 hpa. Samples were treated with Romidepsin.

value: Romidepsin


title: ROMIDEPSIN 6hr replicate 3


title: D15_serum_GDF9_exp_R3_C2 (scRNA-seq)


title: D15_serum_GDF9_exp_R3_C1 (scRNA-seq)


title: D15_serum_GDF9_exp_R2_C3 (scRNA-seq)


title: D15_serum_GDF9_exp_R2_C1 (scRNA-seq)


title: D15_serum_GDF9_exp_R2_C2 (scRNA-seq)


title: D15_serum_GDF9_exp_R1_C2 (scRNA-seq)


title: D15_serum_GDF9_exp_R1_C3 (scRNA-seq)


title: D15_serum_GDF9_exp_R1_C1 (scRNA-seq)


title: ROMIDEPSIN 3hr replicate 2

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 3 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails, at 3 hpa. Samples were treated with Romidepsin.


title: ROMIDEPSIN 6hr replicate 2


title: TBP_JP2NTOE ChIP-seq

source_name: Heart

value: Heart


title: CONTROL 6hr replicate 2


title: TBP_Control ChIP-seq


title: MEF2_JP2NTOE ChIP-seq


title: MEF2_Control ChIP-seq


title: JP2NT ChIP-seq Replicate2


title: ROMIDEPSIN 3hr replicate 3


title: JP2NT ChIP-seq Replicate1


title: ROMIDEPSIN 72hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 72 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 72hpa. Samples were treated with Romidepsin.


title: ROMIDEPSIN 72hr replicate 3


title: ROMIDEPSIN 72hr replicate 2


title: Gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

description:
sorted cells from small intestinal crypts (M01)
Extracted RNA from gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

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. CEL-Seq
Genome_build: mm10
Supplementary_files_format_and_content: coutc files contain raw counts (not normalized)

source_name: murine small intestinal crypts

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing (Samples Neurog3ChronoBulk01-06) or on an Illumina Hiseq4000 using 150bp paired end sequencing (Samples Neurog3ChronoBulk09-16)

value: Neurog3Chrono hom

value: intestine

tag: sequencing

value: NextSeq500 75bp paired end

tag: barcode number

tag: barcode sequence

value: TGCATATC


title: ROMIDEPSIN 3hr replicate 1

tag: treatment


title: CONTROL 72hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected at 72 hours post amputation.

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails at 72hpa. Samples were untreated.


title: CONTROL 3hr replicate 2

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected 3 hours post amputation.

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails, at 3 hpa. Samples were untreated.


title: CONTROL 72hr replicate 3


title: CONTROL 72hr replicate 2


title: CONTROL 72hr replicate 1


title: Gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

description:
sorted cells from small intestinal crypts (F03)
Extracted RNA from gate 1 (green) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

tag: genotype

tag: strain

value: GTACGCGA


title: CONTROL 6hr replicate 1


title: CONTROL 3hr replicate 1


title: Gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

description:
sorted cells from small intestinal crypts (M01)
Extracted RNA from gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 2

tag: tissue

value: ACTGAATC


title: ROMIDEPSIN 72hr replicate 1


title: CONTROL 3hr replicate 3


title: Gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

description:
sorted cells from small intestinal crypts (F03)
Extracted RNA from gate 0 (negative) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

value: CAGTCCGA